


The Perfect Choice

by Tarlan



Category: Stargate Atlantis
Genre: Alternate Universe - Canon Divergence, M/M, Romance, Stargate Atlantis Big Bang Challenge
Language: English
Status: Completed
Published: 2012-10-03
Updated: 2012-10-03
Packaged: 2017-11-15 13:45:22
Rating: Explicit
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 25,460
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/527954
Author URL: https://archiveofourown.org/users/Tarlan/pseuds/Tarlan
Summary: <blockquote class="userstuff">
              <p>Instead of returning to the SGC after the Anubis incident, Rodney stays in Siberia, and Elizabeth chooses Kavanagh to be her chief of Science for the Atlantis Expedition. Having designed and built the <i>Daedalus</i>, Rodney persuades O'Neill to let them go search for the missing Atlantis Expedition.</p>
            </blockquote>





	The Perfect Choice

**Author's Note:**

  * Inspired by [The Perfect Choice](https://archiveofourown.org/works/533028) by [Valika](https://archiveofourown.org/users/Valika/pseuds/Valika). 



> With many thanks to **aqualegia** , **siluria** and **taibhrigh** for their wonderful beta skills!

**Siberia:**

Rodney pulled his orange fleece tighter around him and wished the laboratory had better heating. After the Anubis incident he had hoped he would be transferred back to the SGC, or failing that, to Area 51; but Hammond had booked him on the next flight back to Russia. Admittedly, he had a lot of research projects running in the top secret Siberian complex that he'd been exiled to after the Teal'c incident, but he was 85% positive that at least one of his Russian counterparts could manage to take them over without blowing up half the planet.

According to Colonel Chekov, the Russian liaison to the SGC, that wasn't sufficient reassurance, so he was sent back to finish his work on the Mark IV Naquadah generator. He was designing the generator in parallel with Scientist Rozhkov, who had his own ideas on how to proceed. Of course Rodney's ideas were better as he had decided to redesign the Mark IV from scratch rather than try to improve on the output of the Mark III. His version was smaller - portable - and yet more powerful than its predecessor. It was a worthy project requiring his genius, but he couldn't help wishing he was completing the work in far warmer climes. After all, he had left Canada to get away from the cold Toronto winters.

"Doctor McKay."

Rodney sighed and turned to face the Russian colonel who ran security for the complex. "Colonel Leonov." He only remembered the man's name because it was the same as the spaceship in _2010: Space Odyssey_.

The handsome colonel smiled almost pleasantly, as if welcoming him back. "Perhaps you will accompany me to the main testing laboratory."

Rodney frowned as no one had mentioned any tests taking place before he was recalled to the SGC, and he didn't think the five days he had spent away from this complex would have altered that in the slightest. Despite starting from scratch, he thought his own work was far closer to the testing phase than Rozhkov's more cumbersome redesign, though he had overheard someone mention that Rozhkov had made a breakthrough while Rodney was in Colorado. Even so, it was still too early for either of them to start large scale testing in the main test lab.

"Doctor McKay?"

It sounded like an invitation but Rodney knew it was an order so he sighed again, heavily, and followed Leonov along the cold, utilitarian corridors towards the main test lab. The complex was no more homely than the SGC with its concrete walls covered in peeling paint and tiled floors. Likely, the Russians had built it during Stalin's regime of terror, using it to house the more intelligent political prisoners so Stalin could benefit from their brilliant minds while curtailing their freedom of speech. Certainly, Rodney felt like one of those Gulag prisoners, working from dawn to dusk with very little privacy, and with no decent after hours entertainment other than smuggled in Hollywood movies and vodka.

He had almost forgotten what it was like to have sex with anything other than his own hand.

On the one occasion when he'd tried to flirt with Polina - a particularly lovely scientist with great breasts, who specialized in metallurgy and wasn't completely useless - he'd gained a slap to his face and a threat of more physical violence from her intended husband. Yet how was Rodney to know she was already engaged and planning her wedding? After two years in Siberia, his grasp of the Russian language was well above the basic level, but he was never invited to any social functions, and never included in any of the gossip - unless it was about him. Not that he was interested in gossip.

To them he was _that American_ no matter how many times he told them he was Canadian.

Colonel Leonov ushered him inside and Rodney frowned at the scientists gathered around the main chamber. Moving forward he stopped and gaped as he watched that idiot, Rozhkov, keying in the main sequences on Rodney's prototype of the Mark IV. A quick glance at the readings did not fill Rodney with any sense of security and he stepped in fast, pushing Rozhkov aside.

"What do you think you're doing?" he yelled in Russian. "Are you trying to blow us all up? In which case, well done! You'll probably succeed within the next two minutes."

Rozhkov began yelling back, but Rodney didn't need to recognize the words to understand their meaning as it was clearly expressed in the anger and contempt on his face. It was obvious that he hadn't anticipated Rodney's return today, and that angered Rodney even further. Others joined in on Rozhkov's side and he caught occasional words aimed at him - _arrogant_ and _bastard_ \- before Leonov stepped in looking just as annoyed.

"Perhaps you can explain why you have interrupted Scientist Rozhkov's test?"

Rodney grabbed the screen and turned it to face everyone. "THIS! This is the reason!" He stabbed his finger at the figures scrolling below the main data, and a few of the more intelligent scientists began to frown; Rozhkov stabbed his finger into Rodney's chest.

"You know nothing, _American_. It is within tolerance. Go back to your white board and equations. Leave the real science to those who understand."

Rodney gritted his teeth in anger, bristling at the insult because he was far more than a theoretical astrophysicist. Rodney knew the tolerances better than any person alive because he had designed and built this prototype, including the program and interface - and Rozhkov's blatant attempt to steal his work was unacceptable and dangerous. Yet Rodney knew the other scientists would band together against him, probably under some misguided idea that they would be reaping the rewards of his vast intellect in the name of Mother Russia rather than sharing the technology with the Americans. Rodney looked to Leonov for support, hoping the Colonel might be more cautious, and he read indecision.

"Colonel?"

Leonov had seen Rodney's Mark IV prototype in his lab just before the SGC recalled him to help with the Anubis problem. He had to know that this was not Rozhkov's work, and that Rodney knew what he was talking about.

"Don't let him do this," he implored. "Or better yet, wait until I'm far enough away from this facility, like on the next plane back to the United States, before you let him input that final sequence. No one will miss his minuscule intellect, whereas I might be the last hope for saving the planet one day... again."

Leonov sighed heavily. "Step away from the prototype, Scientist Rozhkov."

Rodney wilted in relief. "Thankfully one of you has a modicum of intelligence in this winter wasteland," he remarked, relieved that he wasn't going to die today after all.

When Rozhkov began to argue, Leonov simply rested his hand on his sidearm, and Rozhkov stalked off angrily. "All of you; leave. Go back to your work."

Once the main test lab had cleared, Leonov turned to Rodney with a speculative glint in his eye. "Will it ever work?"

Rodney resisted the urge to answer that question with the contempt it deserved. "Of course. It will once I've stabilized the core."

Leonov nodded and this time his speculative gaze dipped from Rodney's eyes down the length of his body and back up. It shouldn't have affected Rodney, who was convinced right up until that moment that they were both very, very straight, but the lust in Leonov's almond-colored eyes was enough to set Rodney's pulse racing. No one had ever looked at him so hungrily before, no matter how much he had fantasized to the contrary whenever he saw Sam Carter.

Nervously, he hooked a thumb over his shoulder. "I should be heading back now. To my lab."

Leonov nodded and Rodney walked away briskly, but he couldn't resist glancing back to find Leonov still watching him with an enigmatic smile.

Strangely, Rodney wasn't surprised when Leonov showed up at his quarters later that evening. With a little apprehension, he let him in, and when Leonov finally left Rodney's bed just before dawn, Rodney stretched and sighed at the pleasant ache in his ass and the release of tension in his body. He dwelled for a moment on the night before, and on Yuri's gentleness. Yuri had made it abundantly clear that Rodney could call a halt to it at any time, and he would respect his wishes. Several shots of vodka had helped calm his nerves and he licked his lips as he remembered the taste of the spirit on Yuri's lips and on the tongue that twined with his own in that first deep kiss.

Rodney had found himself receptive to Yuri's gentle coaxing, arching into the strong hands caressing him and learning more about sex in that one night than he had since puberty. Admittedly, Yuri was his first male sex partner but, surprisingly, the absence of breasts hadn't mattered in the slightest once Rodney had filled his mouth with a thick cock instead of a taut nipple.

By the end of that first week, Rodney had no doubts left that he was bisexual, seeing it as a distinct advantage as he was no longer restricted to finding a partner from only the female half of the population. If anything, he wondered if he might be leaning towards his own gender as he soon discovered that the only thing better than thrusting into Yuri's tight ass was being fucked in turn by the hot Russian colonel.

For the first time since arriving in Russia in exile, he was actually happy to be there.

Five days later, Rozhkov killed himself and fifteen others when he went against orders and fired up Rodney's Mark IV prototype while Rodney was in Moscow defending his work to their equivalent of the SGC. The Russians decided to hand the project over to the Americans and Rodney was reassigned to Area 51.

Colonel Yuri Leonov was killed in the explosion.

*****

**Afghanistan:**

John bowed his head as the military court gave its verdict and passed sentence, uncertain if he should be grateful or upset for the black mark placed in his record. He knew his career was over. He would never see another promotion, but at least they had not dishonorably discharged him, accepting partial mitigating circumstances. Instead they had left it up to him to make the honorable decision regarding his future in the US Air Force.

His JAG lawyer stacked the files back into his briefcase. "Under the circumstances, you got off lightly, Major."

"Yeah." He shook DiMarco's hand and walked away, holding inside the terrible guilt and loss that he felt for Captain Holland, who hadn't been so lucky.

He knew they expected him to tender his resignation rather than accept the reassignment to McMurdo - exchanging the precarious yet exhilarating med-evac duties of the front line in Afghanistan for duty as a glorified taxi service in Antarctica - but he wasn't ready to quit. He wasn't ready to head back to the States with his tail between his legs and take up some desk-bound job in his father's multi-million dollar empire; and he wasn't ready to give up the skies, even if the world below would only be the unbroken sheets of ice on the Hut Point Peninsular of Ross Island for most of the year. Instead, he accepted his punishment, flying out on the first available transport, and finally settling onto the uncomfortable bench seat inside a cargo plane for the last leg of his journey from Christchurch in New Zealand to McMurdo.

The flight was bumpy and as uncomfortable as he had expected but the cold, crisp air of Antarctica soon cleared his muggy head.

"Welcome to McMurdo, Major." 

John ignored the ache in his bones from the hard bench seat and returned the salute to the duty sergeant, knowing this would be the only warm welcome he received. His new commanding officer had already tried to have John's duty assignment rescinded, not wanting a pilot who couldn't take orders. John knew he wasn't wanted here; he also knew he would be unlikely to find to find any C.O. willing to give him a second chance except under duress.

Arriving in his C.O.'s office, he saluted and waited to be told to stand at ease. It was a long time coming as Colonel Hepson scrutinized him from head to toe.

"Get a hair cut, Major, then report to Major Stilson for duty."

"Yes, sir." John saluted again but couldn't resist a little sloppiness - not enough to get him put on report but enough to irritate the Colonel.

Stilson turned out to be another pilot, controlling the schedule of flights to and from the various research facilities in Antarctica.

"We'll start you off on the milk runs, Sheppard. Let you get your bearings."

Perhaps pilots were a different breed to the rest of the military because they liked each other almost immediately, understanding the need to never leave a man behind even if that meant taking questionable risks.

At first the frigid air was unbearable after the heat of Afghanistan. It didn't seem to matter how many layers he pulled on, he wasn't able to banish the cold that seeped into his bones. Eventually he began to acclimatize, slowly removing layers until he no longer looked like the Stay Puft Marshmallow Man from _Ghostbusters_. For the most part John kept to himself, aware that others knew about his black mark and finding it still too raw a wound to discuss, even with Stilson. In Afghanistan, he had lost three good men in close succession, and though two of them had been his best friends since flight school, losing Holland had hurt the most. Perhaps it was because there had been nothing he could do for Mitch and Dex, seeing their helo destroyed just after it touched down outside of Kabul.

For Holland he had disobeyed orders and taken the greatest risk, refusing to leave the wounded pilot behind enemy lines. If he had succeeded - if he had saved Holland and brought him home alive - then John suspected they would have pinned a medal on his chest, but he had misjudged the amount of enemy firepower and had been forced to crash-land his helo. He'd located Holland and had tried to walk them both out of the desert but the Taliban had also been out looking for them.

Holland had died of injuries that would not have been fatal if John had managed to evade the Taliban insurgents and got him to the medics on base. Instead they had both rotted in a tiny padlocked cell under heavy guard until Holland succumbed to an infection. John was left to face the humiliation and beatings alone until a SEAL team stormed in and brought him home.

According to his less than pleased ex-Commanding Officer, if it had been up to him then John would have been left to rot inside that cell. Instead John had his father to thank for exerting political pressure on the military to effect his rescue. Some would see it as love for his son but John knew it was just one more excuse for his father to call him a failure, and demand he resign his commission and return to where his father felt he truly belonged - behind a corporate desk with his brother.

The months passed by quickly and John was surprised to find he enjoyed the solitude and the sheets of ice beneath his helo. There was something clean and untouched about Antarctica. The world beneath him was pristine white, and the sky above was often a cloudless blue. It was beautiful and peaceful - a balm to his battered soul. Over the next few months he felt the tension of Afghanistan drift away, quickly recognizing the few landscape features beneath him as he taxied scientists and military to and from the various scientific stations. Even his C.O. had begun to thaw towards him. He filled his off duty time with occasional games of poker, reading, catching up on movies and TV shows, or having a drink with some of the other pilots in Gallagher's bar. It was there that he first heard about the strange events sixty or so miles away across the ice of Ross Island.

"What did you see?" John asked.

Stilson shrugged his shoulders. "Not much. Just lights in the distance, possibly mid-air explosions. Like an aerial battle. I started towards the area but Hepson ordered me back to base."

"A battle?"

John sat back with his drink and frowned, wondering which countries were involved. Everyone wanted to lay claim to Antarctica but under the Antarctic Treaty, signed by around fifty countries, they had all agreed to prohibit military exercises, mining, nuclear testing and waste disposal. Military personnel were only allowed for scientific research or, like him, for ferrying cargo and passengers to the various research bases. He guessed that there was always a chance that one of those countries had broken the treaty but John thought they would have heard of any worsening political situations much earlier than this, especially in such a close knit place at McMurdo.

With not much more to say, the talk turned to other topics. A few weeks later, John was given a new task by Stilson.

"Need you to take out the Osprey."

Stilson handed him the itinerary and John was intrigued when he noticed he would be flying out towards where Stilson's aerial battle was supposed to have taken place. It had been an unofficial no-fly zone since Stilson's report of strange lights. On board the Osprey he carried fifteen civilian scientists and additional cargo. He was very surprised when he reached the coordinates to see a dome already in place. He guessed that one of the other Antarctic bases must have flown in the tents and structures, though John hadn't heard anything about it until now, which was strange as McMurdo was the closest base. Seeing mainly US military on the ground made him even more curious, wondering why they had not gone through McMurdo.

Any chance to investigate was hampered immediately with orders to head straight back to McMurdo.

Over the next few months he flew out in that direction more regularly in the Osprey, though sometimes he _borrowed_ one of the Canadians' smaller helos if it was just ferrying a few passengers. They never let him stay though; never let him know what they were researching on or beneath the ice. It intrigued him but the military had taught him how to keep his curiosity in check. It was classified as _need to know_ , and according to them, he didn't need to know.

That all changed when General O'Neill arrived at McMurdo and John was assigned to take him out to the outpost.

As he deployed evasive maneuvers, all of his training came back to him as naturally as breathing. Over his headset he could hear O'Neill giving orders, but John was the man at the stick and although O'Neill was a trained fighter pilot too, the General was used to jets not helos. John knew the only way out of this was to use all three dimensions and the ability to simply stop and drop on a dime if necessary.

Gaining them the extra few seconds they needed, John brought the helo down hard into the packed snow and cut power to the engine.

"Sir? What the hell was that?"

But O'Neill was watching the sky and holding up a finger, telling him to wait.

Ahead of them, the strange drone dropped out of the sky, hitting a snow bank and sliding across the ice right at them. They leaped out of the helo in different directions and John spluttered from taking in a mouthful of snow. When the big boom didn't happen, he glanced under the fuselage and saw O'Neill just on the other side of the helo. The drone had finally come to a halt right by his outstretched hand, seemingly inert. John stood up and dusted off some of the snow before making his way around to O'Neill.

"That was different," he stated.

"For me, not so much," O'Neill replied and John had a strong feeling that he wasn't joking.

He watched as O'Neill picked up the strange, squid-like drone before climbing back into the copilot's seat. With a shrug, John trudged back around and climbed into the pilot's seat. He started her back up and moments later they were in the air, heading towards the research outpost. At least John had some of his curiosity sated now, knowing they had to be building and testing new weaponry at the outpost as he had never seen anything similar to the squid-like drone before - only that went against the Antarctic Treaty so it was little wonder that the US military was keeping quiet about their research. When they finally reached the outpost, O'Neill didn't tell him to wait or head back, instead he ordered John to follow him.

The small elevator ride brought him to the most amazing sight and a sense of home that he had never felt from any place before, and he barely heard - let alone acknowledged - O'Neill's order not to touch anything. He could feel something tickling at the back of his mind, calling to him, and he wandered through one large chamber towards another that was surrounded by stunning architecture that seemed to be influenced by many ancient cultures from both the East and West. All of it looked pristine as if recently constructed, and yet it felt ancient. Voices drew him in and he smirked a little, deciding to toy with the guy with the Scottish accent who had just admitted to being the one to fire that drone at them.

The tickling sensation was not just in his mind now. He could feel it in his blood and rippling along his spine. He felt drawn to the strangely ornate chair, only half-listening as Beckett talked about Ancients and their genetics. He ran his hands along the chair, poking at the jelly-like control panel on one arm that seemed to beckon to him. The urge to sit down was too strong and he brushed off Beckett's concerns, only coming to his senses when the chair tilted back and glowed a brilliant blue.

Beckett looked just as stunned as John before he raced off, frantically calling for others.

The whispers in the back of John's mind were soothing, almost muting the pounding of feet approaching from several directions at once. An angry, pony-tailed man in a purple fleece yelled at him.

"Get out of there! You stupid-."

And John began to sit up.

"Belay that!" He heard O'Neill order and this time he wanted to obey, wanted to sink back down into the soothing sensation inside his head.

"This is a dangerous piece of equipment and-."

"Kavanagh? Shut up." O'Neill ordered the still arguing man before he took a few more steps and stood over John. "Major? Think about where we are."

A holographic image of the Earth formed above his head, spinning slowly and gradually zeroing in on Antarctica until it was mapping out the outpost in even greater detail.

Awed and yet confused, John stared up at the display. "Did I do that?"

*****

**Earth:**

Nobody questioned Rodney when he gave the Mark IV a nickname of the _Leonov_ , especially after a few American nerds assumed it was named after the fictional spaceship and passed that around. After all, a dead Colonel from a Russian science base explosion in Siberia was barely a footnote in the scientific community. Most of Rodney's colleagues focused on the more well known scientific personnel lost that day - Rozhkov, Mikel Davidov, and Polina Koroleva.

When SG-1 located the Ancient outpost in Antarctica, just in time to destroy Anubis's fleet, Rodney had hoped to be one given the opportunity to lead the research. He was the closest thing they had to an expert on Ancient technology, surpassing even Sam Carter for obvious reasons. He had spent the past few years studying the Stargate and working with Naquadah to produce the _Leonov_ Mark IV - for even Rozhkov's fatal stupidity had not halted that work. The end result was a portable generator with enough power to light up a small town for years. He figured they could replace the entire Manhattan energy grid with a dozen of these generators and not have to worry about nuclear waste.

His work with Naquadah and his knowledge of the Stargate should have made him the perfect candidate for the Ancient Outpost assignment but, once again, his past failures had caught up with him and they had offered the post to Kavanagh instead.

Kavanagh!

Rodney fumed at the snub. He could think rings around Peter Kavanagh even on his worst day. He sighed in annoyance. Perhaps if Hammond had brought him back from Russia after the first Anubis incident then it would have been him working closely with Doctor Weir after she took over command of the SGC. Instead she had come to rely upon Kavanagh and Bill Lee to keep the scientists in order, so Kavanagh must have seemed the obvious choice when Sam Carter turned down the opportunity to study the Ancient Outpost. It appeared that her focus was more on finding a way to take the Ancient database out of O'Neill's head... again.

Rodney crossed his arms over his chest. "You realize they are wasting a great opportunity here," he ground out, only to see the squirrelly little Czech scientist with the crazy hair shrug.

The Czech sighed. "Kavanagh is an American. They want an American."

"Kavanagh wouldn't recognize a piece of Ancient technology if it stood up and bit him on the ass."

"But he is perfect secretary. Yes? Good at paperwork and pen pushing."

Rodney harrumphed as that summed up Kavanagh perfectly in his eyes. The man was an adequate scientist especially in biometric fields, but he lacked imagination and spent too much time focusing on trivial matters and office politics for Rodney's liking. Perhaps that was what Weir needed though - a scientifically minded bureaucrat to run the Outpost's science department.

Several months later, Zelenka, whose name he had finally learned, slid a filled mug of coffee across the desk, drawing Rodney's attention away from the schematics he was working on. Zelenka was one of the few people Rodney could tolerate - and who could tolerate him in return, even on a bad day. Rodney found him an incredibly useful sounding board for ideas, able to follow his train of thought for the most part and even make not so incompetent suggestions. They fought on occasion - viciously - but with passion for science rather than malice. He liked Radek, and if Radek hadn't been as straight as they come then Rodney would have married the man... or at least taken that passion into the bedroom.

"I hear rumor that Colonel O'Neill is no longer Popsicle. He is now General O'Neill in charge of SGC."

Rodney frowned as he considered that news as it meant that Hammond had either retired or gone on to _better_ things. Not that Rodney was that interested in cashing in a favor owed by O'Neill and asking to be reassigned to the SGC. He had saved O'Neill's life during the first Anubis incident by re-coding the X302's ejection sequence. It had given O'Neill the precious few seconds he needed to eject before the X302 opened and entered an unstable wormhole with the overloading Stargate.

At least in Area 51 Rodney was in charge of his own department rather than being forced to listen to the verbal diarrhea of scientists like Lee, Kavanagh and Felger.

Another few months passed before news filtered in that Daniel Jackson had uncovered the address for the Lost City of the Ancients: Atlantis.

"The city that sank beneath the waves," Rodney murmured softly.

As a kid he had loved listening to old myths and legends, and if he hadn't discovered an affinity and love for math and the stars then he might easily have gone into the soft sciences, like Daniel Jackson. As much as he pretended to despise the soft sciences, he still felt a pang of regret when he learned that some of those old myths were based in fact. Merlin - Myrddin - had been a real person, an Ancient who had ascended and then returned, somehow keeping all of his memories. To the humans of that time he must have seemed like a magical being - a wizard - able to conjure light from nothing.

Every scientist in Area 51 wanted to go to Atlantis until they learned it might be a one way trip. Rodney was surprised when he received an email offering him a position on the expedition, but the very thought of working under Kavanagh was too terrible to contemplate so he swiftly turned it down. He had carved out a small niche for himself in Area 51 after the success of the _Leonov_ , and was already deep in the process of designing the first of Earth's deep space carriers.

The Daedalus-class 304 battleship would integrate Earth and Asgard technologies, including Asgard Naquadah-cored hyperdrive engines. It was a unique opportunity for Rodney to work directly with an actual Asgard and learn even more about their technology. Perhaps if circumstances had been different then he might have given up that opportunity to instead be one of the first people to step into the fabled lost city of Atlantis in more than ten thousand years - but not with Kavanagh in charge.

"Atlantis... The city that sank beneath the sea," he murmured to himself again that night, half-filled with regrets.

Certainly he felt a pang of regret for turning down the Atlantis offer so quickly but he knew that the chance to work on the 304 with the Asgard was just as incredible. Still, Rodney was surprised when Zelenka accepted a position on the Atlantis Expedition as one of its lead engineers. It was a shame because Radek was still one of the few people who could almost keep up with Rodney on occasion, and he was an exceptional mechanical engineer. Rodney had hoped to convince him to become his deputy on the _Daedalus_ Project.

"You should come to Atlantis too, Rodney, despite Kavanagh. Perhaps the city will be large enough to accommodate both of your egos."

"Oh ha, ha. It's a one way ticket to another galaxy with Kavanagh in charge," Rodney countered. "And I'm certain my large _intellect_ ," he stressed, "will be more usefully employed building Earth's first deep space battle cruiser."

Radek sighed.

"Promise me one thing then, Rodney. Do not forget us. If you do complete your precious 304 then convince the SGC to send it to Atlantis. Then it will not be a one way trip for the rest of us, ano?"

Rodney folded his arms and sighed. "I'll think about it."

"Good luck, my friend."

Rodney saw the hand Radek held out towards him and sighed again, this time with sadness tinged with regret. "Good luck."

They shook hands and Rodney watched Radek walk away, wondering if he would ever see him again.

Four weeks later, over eighty scientists and soldiers stepped through the Stargate to Atlantis, taking a number of Rodney's _Leonov_ Mark IVs with them. Rodney returned to his schematics and as the days stretched to weeks, he concentrated on the Daedalus Project, and his promise to one of the few people he could call _friend_.

What he did discover was that the Asgard were no different than some of the scientists he had worked with over the years. Admittedly, he and Hermiod came to a mutual understanding and a certain level of respect for each other's intelligence after a few _arguments_. Plus the arguments had the added effect of taking away any awe that Rodney might have felt towards the far older, little gray alien with no clothes - or genitalia. Instead they settled down into a pretty good working relationship.

Rodney got to see a lot more of O'Neill than he had anticipated, and he noticed that despite the lack of PhDs, a lower IQ than his and Hermiod's, and a certain flyboy nature, Hermiod always treated O'Neill with the utmost respect. Hermiod seemed to like Jackson as well, and it went without saying that he - it - liked Sam. Rodney couldn't think of anyone who didn't like Sam because she was smart, beautiful and, unlike him, was happy to share her toys and knowledge.

Perhaps it was the whole Anubis incident and that Platonic kiss on the cheek, but Rodney had found himself less attracted to Sam these days, taking on a sibling rivalry instead. He still played it up heavily just to annoy her, but judging by her indulgent smiles, he had a feeling that she had started to see through the ruse.

"Sam?" He called her attention to the coding for the navigation system, knowing something wasn't right but needing a second pair of eyes to confirm his suspicions. She caught it the moment he pointed out the subroutine that was bothering him.

"Yes, I see it," she murmured and between them they re-coded Felger's subroutine, sparking ideas off each other the way Rodney used to work with his sister, before she decided that marriage and kids were more important than being a world-renowned theoretical physicist. For a moment he wondered what it would be like to get married and have kids, and he eyed Sam curiously.

She caught his look and narrowed her eyes questioningly.

"I was just wondering what we'd be like married."

She tilted her head to the side in contemplation. "I'd give it six months before I tried to kill you in your sleep."

"Six months? I put it closer to four."

She smiled brightly and they went back to work, arguing over the next piece of code, and if she did call him petty and arrogant on more than one occasion, he let that slide right off as he called her a dumb blond in retaliation.

****

**Atlantis:**

Those first few days on Atlantis had proved difficult. It was clear from the moment they stepped into the city that Kavanagh did not have a clue how to proceed. It wasn't that he was a bad scientist but simply that he did not have the depth or breadth of knowledge needed to deal with the hundreds of small things that went wrong - or the ability to think outside the box.

When the shield began collapsing the moment they arrived, Kavanagh panicked leaving a Czech engineer to pick up the pieces and get all of the scientists organized. Fortunately, instead of the shield collapsing completely and crushing them beneath the weight of water, once the city reached a critical point it rose majestically from the ocean bed to the surface. Kavanagh insisted that he'd known that would happen all along, and the ensuing fireworks between him and Zelenka had needed Doctor Weir's intervention, but it was obvious to John that the rest of the science contingent had started looking to Zelenka for orders and answers rather than Kavanagh. In the end, Kavanagh became a puppet chief of science while Zelenka did all the work, and Weir merely kept up the pretense that Kavanagh was in charge of that area.

It wasn't Weir's only mistake in those early days but it was the one that lost her the greatest amount of respect from everyone. Sumner treated her with barely veiled contempt most days, and in some ways that had made John her ally as Sumner treated him with that same disdain. John found himself sidelined most days, spending his time alternating between paperwork as Sumner's unwanted second-in-command, and on light-switch duties for the scientists the rest of his time.

The majority had truly believed that they would find a stash of those ZPMs sitting by the Stargate when they arrived in Atlantis, so it was a shock to most when they discovered they were cut off from Earth indefinitely. When their supplies began to dwindle and small fights started to break out over the few remaining luxury items, John approached Sumner.

"We ought to set up a few more off-world teams. See if we can barter for food and other essential supplies."

Summer narrowed his eyes but John knew he had a point. At the rate they were going through the supplies brought with them from Earth, they would be starving within another month. As it was, they were already rationing coffee and other items, and no one had anticipated how quickly some of the scientists would get through uniforms - damaged through fixing problems in the city.

"Set up three teams and coordinate the requirements from Doctors Weir and Kavanagh. I'll lead the first team; Lieutenant Ford and Sergeant Bates can take the other two."

"Sir, maybe I should lead-."

"You're more useful here, Major."

Sumner's excuse was that John was needed in the city because of his ATA gene but John knew it had more to do with the black mark on John's permanent record. Even though John had given Sumner no reason to doubt his obedience to Sumner's chain of command, the stigma of that black mark remained.

At least his light-switch duties were reduced when Beckett figured out a way to give more people the ATA gene, but that only left him with even more time on his hands and he began to regret his decision to join the expedition. He missed flying. Flipping a coin had seemed like a great idea at the time but now he wished he had not left such an important decision to chance.

The gene therapy didn't take with either Kavanagh or Zelenka - sadly in Zelenka's case as of all the people who truly needed the gene, he was top of John's personal list. He decided to seek out Zelenka and offer his commiserations, and found him in the Gateship Bay above the Gate Room. He stood at the bottom of the open ramp and gazed inside, smiling wryly when he saw Zelenka on the floor with a panel removed.

"Heard the news," John stated softly, and Zelenka looked up at him, blue eyes blinking owlishly through thick lenses.

Zelenka shrugged in fatalistic resignation. "It was not to be. Beckett will continue to work on it. Maybe one day..." He shrugged again.

"I wish it had worked for you though."

Zelenka took off his glasses and rubbed at tired eyes. "In truth, if I had one wish it would be for Rodney McKay to be here instead of Kavanagh."

John walked a few steps up the ramp and leaned against the gateship. "McKay? Someone you knew in Area 51?"

"Brilliant scientist... though I would never say so to his face. Very big ego," Zelenka added and sighed, "But well deserved."

"So why wasn't he invited?"

Zelenka's lips twisted into a half-smile. "He was. He was offered a place on expedition but would not work for Kavanagh."

"Yeah. Kavanagh isn't one of my favorite people either."

John looked away, glancing at the gateships sitting in their bays as he felt that itch in the back of his mind that seemed to draw him towards all Ancient technology. Zelenka had spent hours working on them, looking through the dead circuitry when he ought to have been resting. He looked back up at John.

"They had a gateship at the SGC but no one had tried to operate it." Zelenka gave him a calculating look. "Perhaps you would wish to try? Yes?"

John licked his lips in fascination, feeling that call thrumming deep inside that beckoned him towards the cockpit. He had answered that call once before and ended up in the control chair in Antarctica, and now it called to him again. He moved forward and gently laid his hand on what he hoped was the pilot's controls, thinking ON. The panel lit up immediately, and images swept through his head: temperature, air pressure, vacuum seals, energy levels, weaponry. Too much information too quickly and he found himself ordering it to slow down... and it did.

He glanced around and found Zelenka grinning insanely. "Do you think you could fly her?" Zelenka asked.

John slipped into the seat that he now knew was the pilot's, and just like with the chair, he brought up a screen: the HUD. He felt rather than saw Zelenka drop into the copilot seat, and changed the information displayed according to Zelenka's questions. The urge to actually take flight was so strong that he almost gave into it. Instead he felt the gateship rise several feet off the bay floor, hovering more easily than any helicopter, and all with just a casual thought.

"What's going on here? No one was authorized to touch these gateships."

John set the ship back onto the deck and sent an OFF message before glancing over his shoulder. Kavanagh strode up the ramp with a thunderous expression and John decided to let Zelenka duke it out with his boss. After all, he was just the light-switch here even though he still felt the pull of the little ship in his mind. Admittedly, part of that was his own desire to take to the air, missing the blue skies and the freedom of flight more than he had ever dreamed.

"You may have delusions of being in charge, Doctor Zelenka, but that authority still rests with me. The gateships are not a priority at this time."

"These ships are not ornaments. They were meant to go through the Stargate," Zelenka stated angrily. "They would be vital in collecting supplies and protecting our people."

"And who's going to fly them?" Kavanagh sneered.

"Me." John spoke up. "I'll fly it."

"And risk losing the person with the strongest ATA gene on Atlantis? No." Kavanagh crossed his arms.

"We need those ships," John insisted. "So far we've not come across any of these Wraith, but once Sumner starts taking out foraging teams, the risk increases."

"What Wraith?" He scoffed. "That was ten thousand years ago. They're likely as dead as the Ancients by now."

"And what if they're still out there?" Zelenka added. "We could at least make certain these ships can fly, if only to use as escape pods, carrying all of our equipment and people."

John could see the doubts crossing Kavanagh's face and hoped he would see reason rather than dig in his heels just to be pedantic.

"One ship. Prove to me that it's flight worthy and I'll consider it."

Zelenka nodded solemnly, waiting until Kavanagh had left the Gateship Bay before turning a jubilant expression towards John.

"Now we get to work," he crowed, and gestured for John to take the pilot's seat once more.

****

**Earth:**

Rodney grinned when Colonel Caldwell gave the order to leave the space dock using maneuvering thrusters. He took a moment to enjoy the stars before turning his attention back to his work station. Diagnostic data from all over the ship streamed across the screens and Rodney read it all with ease having written or at least vetted most of the code.

"All systems within tolerance," he stated.

Something flashed red and Rodney began keying faster, diving into the code and quickly working through the problem to stabilize the Naquadah core, humming happily to himself when the warning light shifted back through amber to green. They had fired up the engines hundreds of times under test simulations and more than a dozen times while in the space dock but this was the maiden voyage of the _Daedalus_ \- her shakedown cruise to the outer edge of the solar system using the sublight engines. She had a skeleton crew on board and didn't even need her captain but Caldwell had insisted on being here. It was his ship after all - not Rodney's despite his tendency to ignore Sam's mocking and call the _Daedalus_ his baby.

On a private channel, Rodney listened to the chatter from mechanical and software engineers all over the ship, interrupted only by status reports from Hermiod, who was manning the engineering controls with Doctor Novak.

"Hermiod is ready to initialize main sublights," Novak stated nervously, and Rodney rolled his eyes when she added a hiccup to the end.

He recalled that Novak had been on board Sam's prototype ship, the _Prometheus_. Rodney had managed to convince O'Neill to send the _Prometheus_ to Pegasus in search of the lost Atlantis Expedition, calling in his one favor and making good on a promise to Radek at the same time. Unfortunately, the _Prometheus_ had never made it after being hijacked en route. Eventually they got the _Prometheus_ back but had to scratch its mission for the time being, much to Rodney's dismay.

Instead of trying to persuade O'Neill to send the _Prometheus_ a second time, Rodney focused his attention on completing the _Daedalus_.

The _Daedalus_ was bigger and faster than the _Prometheus_ , building on some of Sam's work but mostly working to his own specifications with input from Hermiod. She was more than a deep space cargo vessel, and more than a battle cruiser. She had a hyperdrive capable of traveling across the void between the Milky Way and Pegasus in less than three weeks, and the ability to make that trip even faster if they could use the ZPM currently housed in the Antarctic Ancient Outpost - or create another ZPM.

Rodney had several ideas on that score but had yet to find the time to spend on the calculations. He had already determined that the ZPM generated its power from vacuum energy derived from a self-contained region of subspace time - which was more than Kavanagh had managed to figure out after a year studying the Ancients' power crystal. All Rodney had to do now was work out how to build a bridge to that self-contained region and extract the required exotic particles. Annoyingly, this was Jeannie's area of expertise and once more he ardently wished she had not met a damned English major and given up her career to become an everyday housewife and mother.

He was still considering whether it was worth forwarding his theories on to her anyway, even though they hadn't spoken in nearly four years. Although he didn't expect her to forgive him for his words and actions - or non-action as the case may be by refusing to attend her wedding - he hoped she might be intrigued enough by the power equations. Jeannie had always loved solving problems.

By now the Atlantis Expedition had been out of contact for close to eight months.

With the war against the Replicators threatening the stability of the whole of the Milky Way galaxy, the chances of O'Neill sending another ship to find out what had happened to them was remote, especially if a round trip would take a minimum of six to seven weeks. According to the I.O.A., they needed the _Daedalus_ here, supporting the _Prometheus_ as they tried to protect Earth. There were other Daedalus-class vessels being assembled in orbit, overseen by Rodney's team, but it would be months before they came online.

If Rodney could create a ZPM, or something close to the same energy output as a ZPM, then the number of days for the round trip to Pegasus would be greatly reduced, giving Rodney more leverage against the I.O.A..

Rodney glanced up in time to see the _Daedalus_ pass close to Jupiter, momentarily awed by the majesty of the largest planet in the solar system, with its never-ending storm circling its belt. He grinned even as he ducked his head back to his control screens. Maybe there would be time for staring out the view screen on another less intense trip, but for now he really needed to put all his attention on the read-outs and collate all the data from the various departments.

"Well, Doctor McKay?" Caldwell demanded an update.

"So far so good," he breathed out happily, grinning back at Caldwell and gaining a begrudging nod of respect in return.

"Well done, Doctor."

Rodney grinned at the praise, knowing it was well deserved after all the work he had put into this project. They reached the edge of the solar system and turned around in a sweeping arc, slowly heading back towards Earth. The next shakedown would be the real thing, testing out the hyperdrive engines, and Rodney was eager to get the planning stage in motion.

Once back in the space dock, Rodney gloried in the praise coming from all sides, magnanimously adding his own praise for his team.

"Well done, people. Christmas isn't canceled after all."

He heard a faint cheer over the comms and smiled wryly as his own Christmas plans had never included anything other than work. As he was still not on speaking terms with his sister, and she was the only family he possessed, that did not leave him many other options. His last relationship had survived less than two dates, probably because those dates had been three weeks apart with half a dozen broken or forgotten promises in between. Not that he was overly upset at the loss for Graham was no beauty and brains like Sam Carter, or handsome and dashing like Yuri. It had been good to have another hand on his dick other than his own for those two nights though, and it would have been nice to have someone to spend all morning in bed with on Christmas Day.

He had asked Sam but she'd given him that special glare reserved solely for him, and mentioned having other plans for the holidays.

Rodney gathered all the data together, already planning to spend the next few days going over all of the read-outs. 

The _Daedalus_ had fully integrated Asgard beaming technology and Rodney made excellent use of it as he ordered the technician in charge to beam him back down to his laboratory in Area 51. The others on board would ' _beam down_ ' later, once they had completed final checks. As the plain white walls of his office coalesced around him he sighed deeply and opened his laptop, making coffee while it booted up before settling in to study all the results from today's shakedown cruise.

He caught movement from the corner of his eye and walked to the window separating his office from the rest of the laboratory, watching as his remaining staff filed out with happy, smiling faces, talking of plans for the next two days. Several of them glanced over and one even waved. Rodney felt a stab of loneliness as the door sealed behind the last of his staff, leaving him alone in an silent laboratory. He breathed in deeply, letting out the breath in a soft sigh, and ducked his head. Within minutes he was immersed in data, code and equations.

It was Christmas Eve and he had nowhere else to go, except for his lonely apartment.

*****

**Atlantis:**

Christmas Eve on Atlantis was a miserable affair. Bates' team had managed to score some sort of tuber in exchange for Zelenka and a group of engineers fixing the Manarians irrigation system. The tuber was a strange orange color like pumpkin and, fortunately it wasn't too unappetizing, tasting like a cross between parsnip and potato. The botanists insisted it was a good source of Vitamin A.

Earlier John had taken a group of marines over to the mainland in a gateship, and they had managed to hunt down a few of the large bird-like creatures that tasted a little like chicken. It wasn't exactly the best Christmas menu he'd ever seen but he'd faced worse while on active duty in foreign lands, and no one here was complaining as it certainly beat facing another day of MREs.

Christmas Day came and went without incident, but three days later Markham pointed through the cockpit window at the distant horizon as they headed back towards the mainland to hunt.

"What _is_ that?"

John frowned and called up information on the HUD, eyes widening when he realized it was a massive storm front heading straight for Atlantis.

"We're heading back," he stated urgently. "Gateship One to Atlantis. Come in Atlantis."

"Atlantis here."

"We're on our way back. There is a major storm heading our way."

There was a slight delay. "We have it on sensors. I'll inform Doctor Weir and Colonel Sumner immediately. Atlantis out."

John noticed the air of panic as he stepped out of the gateship, and he made his way swiftly to the briefing room where Weir was holding an emergency meeting concerning the coming storm.

"Is there a chance it will just fizzle out or veer off before it hits us?" Sumner asked, looking to Kavanagh for an answer.

Kavanagh looked to his left, to a scientist John had noticed around the mess hall on occasion but had otherwise paid no mind towards. He wasn't one of those constantly demanding John's presence to initialize equipment.

"Doctor Metcalfe is the closest we have to a meteorologist. Doctor?"

Metcalfe looked a little sick with nerves, his hands wringing as he looked around the table. "As far as I can see, it has no reason to fizzle out or veer aside. Perhaps if there was more land mass between us and the storm then that might have affected its path but..." He shrugged.

"So this monster storm is heading right at us. What can we expect?" Sumner asked.

This time Zelenka spoke up. "The city has no defenses against the tsunami building with the storm. It will be swamped."

"Wait," John interrupted. "The Ancients must have had some way of deflecting storms in the past."

Zelenka pushed his frames further up his nose and shrugged apologetically. "The Ancients had a ZPM to raise the shield or lower the city beneath the waves."

"What do we have?" Weir asked.

"Seven Leonovs. Mark IV Naquadah generators," he added for the benefit of those unused to the nickname, and John noticed Kavanagh pulling a disdainful face.

Sumner frowned. "Will that be enough?"

"Possibly. The shield would only need to hold for a minute, perhaps two at most, but it will leave us severely depleted of power..." He drifted off into thought. "Unless I can use the electrical storm to our advantage."

"What are you suggesting, Doctor Zelenka?" Weir asked.

"I worked closely with the designer of the Leonov. Rodney McKay. I believe I can channel the power of the storm through the conduits in the city and his generators. It may be enough to raise the shield without fully depleting the Leonovs. We will still be without power except for key areas in the city but better that than being reduced totally to oil lamps and candlelight, or forced to abandon the city, yes?"

Sumner looked grave but nodded his agreement.

"Under the circumstances, I think it would be advisable to evacuate all nonessential personnel to the alpha site... just in case Doctor Zelenka's plan doesn't work," Sumner stated.

Kavanagh added, "As chief of science, I should go with them. Doctor Zelenka will of course remain behind to execute the plan."

Weir raised both eyebrows at Kavanagh's seemingly cowardly suggestion but had to concede he had a point. "Agreed." She looked to Sumner, waiting for him to give a tight nod of agreement before turning her attention to John. "Major Sheppard, Doctor Zelenka mentioned you have several pilots now fully trained. Perhaps you can assist with the evacuation using the gateships."

"Sure... but if Doctor Zelenka's plan doesn't work then we may need to get him out of the city quickly." He didn't need to remind them that Zelenka was the only one holding Atlantis together most days. "I'm your best pilot, Colonel."

Reluctantly, Sumner agreed, but even he recognized that Zelenka was the best scientist in the city. John was not surprised when Doctor Weir elected to leave too, knowing she would be more useful in helping to set up the temporary encampment on the alpha site.

With only a few hours remaining before the storm reached Atlantis, they swiftly began to evacuate, taking as many supplies and as much equipment as they could manage. They all knew that if Zelenka's plan failed then Atlantis might be lost to them, along with everything they were forced to leave behind.

By the time John had made his third run through the gate, the storm front had reached Atlantis. As he waited for the last of the equipment to be loaded into the gateship for his final run, he listened to the rain drumming on the stained glass window in the gate room. The wind driving the rain had already increased to the point where it would be difficult to fly even a gateship. He worked out a final evacuation plan in his head in case Zelenka's plan failed and they had to leave quickly. The best option was gating to the alpha site but if the city should sink quickly, as it had in the timeline where Weir had gone back ten thousand years, then he might have no choice other than to head straight up through the storm and into space. The closest Stargate was over a week away at maximum speed, and John had ensured he had laid out sufficient supplies for him and Zelenka should it become necessary to make that journey.

He hoped not though, and not because of the thought of spending a week cooped up inside the gateship with Zelenka - Radek was okay, and he played a mean game of chess - but because he couldn't bear the thought of losing Atlantis. For the first time in his life he actually felt as if he had come home. He belonged here among the soaring towers and with the city thrumming beneath his skin, whispering to him, but he knew the city was thousands of years old, and brittle with age. The high winds would cause massive structural damage without the shield to protect it, and if Zelenka's plan to raise the shield just for those few vital minutes did not work then the subsequent flooding would sink the city.

"Major, you're ready to go."

"Thanks, Lieutenant." John gave Ford a nod before squeezing through the piles of boxes to get to the cockpit. Moments later he was raising the ramp and heading down into the gate room. Ahead of him the wormhole was already open as Markham took his gateship through, and John followed moments later, following Markham along the edge of a forest towards the sea. Rising over the low hills edging along the coast, John sighed as he saw the encampment spread out ahead of him. He settled down next to Markham's gateship and lowered the ramp, swinging round in his seat to watch the marines spring into action as they began to unload both gateships.

As soon as they had taken everything, John radioed in.

"I'm heading back. If you don't hear from me in two hours then assume the worst, in which case I'll see you in just over a week."

"Good luck, John," Weir stated, dropping all formality for once.

"See you around, Elizabeth."

The gateship lifted smoothly and within a minute he was dialing up Atlantis from the on board DHD, and diving into the circle of blue. Back in the bay above the gate room, John left the gateship prepped and ready to go immediately, not wanting to lose even one second if Zelenka's plan fell to pieces. For the same reason, he left the hatch open and headed down to see what he could do to assist Zelenka.

In the back of his mind, Atlantis whispered to him, and he wondered if she - it - could feel his growing anxiety as the wind and rain lashed at the towers and heavy swells began to rock the city.

"How's it going?"

"The grounding stations are online. There is nothing more I can do except wait. I estimate the worst of the storm... and the tsunami... should reach us in 33 minutes."

John settled onto a seat beside Zelenka, falling silent for a moment but he could see Zelenka needed his mind distracted.

"Tell me about this McKay?"

Zelenka gave a quick smile. "Ego the size of a small planet." He sighed. "Deserved though. Rodney is a brilliant man... unlike Kavanagh."

"So, really... why didn't he come along?"

"Not enough room in Atlantis for both his ego and Kavanagh's." Zelenka sighed and took off his glasses, wiping them clean with the edge of his shirt. "Given a choice, I would rather it had been Rodney."

John listened as Zelenka spoke of McKay, of his brilliance, arrogance and idiocy. Then he spoke of his friendship and the promise Rodney had made to bring them home if all went wrong and the Atlantis Expedition lost contact with Earth.

"Shame he couldn't keep that promise."

"He is not yet late. If all went to schedule then the _Daedalus_ would only now begin full testing of its navigation and sublight engines."

"Daedalus? Not the Icarus?"

"Daedalus was the man who invented flight. Icarus was the son who abused his father's invention-."

"Flew too high and fell to his death."

"Yes." Zelenka grinned but sobered quickly. "Not many know this but the Leonov was named after a Russian colonel who was killed in a scientific experiment during the development of the Mark IV generator."

"Guilt?"

"No. Rodney was in Moscow at the time of the accident. It was others meddling with his work during his absence."

"So he likens himself to Daedalus?"

"Except with less modesty and more arrogance." Zelenka grinned but John could see that Zelenka actually liked this McKay guy. "It is time."

John nodded and mentally prepared himself as Zelenka watched the screens intently.

"Impact in ten, nine..." Zelenka counted down the last few seconds and John braced himself, feeling the whole city groan as the wave struck. The shield flickered from the force of the water and John gripped the control console harder as the whole city rocked. "Shield is barely holding. Power drain exponential." Zelenka looked to John in fear. "It will not hold!"

"Get ready to move!"

He held on even tighter as the city tilted, sending a mental prayer along the strange connection to Atlantis. "Just a little longer!" 

The city righted itself suddenly, and John went flying across the control room, smashing up against the railing and somehow managing to grasp it as the city seemed to roll with the heavy seas beneath it. He pushed back to his feet and staggered carefully back towards Zelenka, grabbing hold of consoles to keep his balance. Zelenka had managed to keep his seat and though he looked a little green with the swaying motion of the city, his fingers were dancing over the control panel, pulling up schematics and damage assessments.

"We have taken on much water. Lower levels on the east pier are flooded. Breaches in the west and south, particularly where the shield weakened before Atlantis rose from beneath the waves. The damage there is severe."

"Will she stay afloat?"

Zelenka took a deep breath. "Yes. Yes."

John sank back onto the floor and bowed his head, giving silent thanks. "How much longer until it passes?"

"The worst is already passed." Zelenka smiled. "But let us give it one more hour before we recall the others."

That was still within the two hour window that he'd given to Weir so he nodded. One hour, and then he would dial up the alpha site and tell everyone to come home.

****

**Earth:**

Rodney grinned happily as the _Daedalus_ completed her final shakedown cruise. This time next week she would be officially operational and O'Neill had already agreed on her first mission. She would be heading to Pegasus to find out what had happened to the Atlantis Expedition. It appeared that the rumor about O'Neill was true; that he didn't like to leave a man behind - or a whole expedition, in this case.

It had taken a little browbeating but Rodney had managed to convince O'Neill that the _Daedalus_ needed him on this mission, which would be her first intergalactic journey using the pseudo-ZPM - the Zero Point Crystal or ZPC - that he and Jeannie had built together. Rodney estimated that it would take only eleven days to reach Atlantis, which was far better than the twenty-three days using just the Asgard Intergalactic drive alone, though still slower than they could accomplish with a ZPM. Even Hermiod was impressed though the Asgard hid it behind his usual abrasiveness.

"I fail to see why you will be needed, Doctor McKay." Hermiod blinked at Rodney.

"And I fail to see why I would not be needed," Rodney retorted but Hermiod merely blinked again in that passive-aggressive way that he must have perfected over the centuries. Unfortunately for Hermiod, Rodney was no longer in awe of the Asgard, seeing Hermiod as just another - admittedly almost as brilliant as him - colleague.

In truth, Rodney knew Hermiod was more than capable of dealing with any problems arising during the journey to and from Pegasus but Rodney had made a promise to Radek. He bristled a little because promises to Radek aside, seeing Atlantis was his main reason for wanting to be part of the mission. Atlantis: the city that sank beneath the waves - in another galaxy. If Weir had not chosen Kavanagh as Chief of Science then Rodney could quite easily have succumbed to the temptation to head up the science contingent of the expedition. The possibility of it being a one way ticket had always been at the back of his mind but having seen the Antarctic Outpost with its amazing technology and architecture, the very thought of stepping into a city from Earth's myths, that had been lost for ten thousand years, was amazing.

It took him the best part of the week to finish the reports on all of his current experiments and summarize his theories. He made sure his minions could follow on with his ideas despite feeling an almost childish temptation to cling to everything. Carter and others at the SGC had promised that he would retain full credit for the initial work, especially if any of it was published.

Once he was sure no one was going to blow up Area 51, he packed the last of his gear and placed his second and third best laptops into storage, ready to be beamed onto the _Daedalus_. He cradled his best laptop to his chest before sliding it into the velcro pocket at the back of the TAC vest especially created to his specification for SGC off-world teams. Rodney stuffed as much as he could in every pocket, determined to make best use of every inch or space and ounce of his allowance - both personal and work-related.

Unlike the others, he did not need to take the first military plane to Colorado, simply opening a communication to the _Daedalus_ and requesting a beam up. The Asgard transporter beam captured him instantly, and his lab in Area 51 whited out before the transporter room on the _Daedalus_ coalesced around him.

"Welcome back on board, Doctor McKay." The operator smiled warmly, with none of the usual insincerity that he'd come to expect over the years.

"Huh. Thank you."

He was even more surprised when Caldwell met him in the corridor outside with an equally sincere greeting.

"Lieutenant, ensure Doctor McKay's belongings reach his quarters." Caldwell turned back to Rodney. "If you're ready, Doctor, so are we."

"Lead on."

Rodney kept pace with Caldwell all the way to the bridge and stood just behind the command chair as Caldwell gave the order to use sublight engines. They moved quickly through the solar system, though not passing any of the big planets as they headed towards Pegasus. Once clear of the system, Caldwell gave his next order.

"Set heading for Pegasus." He looked up at Rodney. "Doctor, if you wouldn't mind giving the order to put the ZPC online."

With a grin, Rodney moved closer to Caldwell's seat and depressed the communication switch. "Engineering? Initialize ZPC and ready intergalactic hyperdrive."

Novak answered nervously. "ZPC initialized and intergalactic drive readied."

Rodney stepped back and allowed Caldwell to give the final command, feeling confident that nothing would go wrong as he and Jeannie had tested it several dozen times over.

"Engage intergalactic hyperdrive."

The stars ahead of them began to streak as the _Daedalus_ moved swiftly into hyperspace. They were on their way.

After all the excitement, and after verifying that everything was well within tolerance, Rodney excused himself from the bridge and made his way down to the mess for a light meal as he had not eaten for several hours. Then he retired to the small quarters allocated to him for the journey.

He made sure to find a viewport for when they crossed from the Milky Way into the void between the galaxies two days later, and went there several more times over the following days to watch the speck of light ahead of them slowly grow until they could make out the stars of Pegasus. Crossing into Pegasus he watched as the stars thickened in number around them until the stars were streaking past once more. By his calculations, the world holding the lost city was less than two days away at this speed and trajectory, and Rodney could feel the excitement building all over the ship.

****

**Atlantis:**

"Sir? We have an unidentified ship closing fast on our position."

John leaned over the gate tech's shoulder to view the smaller screen before straightening and activating his radio. "Colonel? You're going to want to see this."

Sumner arrived within a minute and tensed when Chuck sent the information to the main view screen. "Wraith?"

"Not according to the Ancient database, Colonel," replied Zelenka, who arrived just a few steps ahead of Kavanagh and quickly took the gate tech's seat, much to Kavanagh's annoyance. John noticed the gate technician smirking.

Kavanagh leaned across him and began tapping in commands, annoying Zelenka who countermanded some of them immediately. The ship's configuration came up on line and Kavanagh turned to Elizabeth, who had joined them.

Kavanagh stood up to face Weir and Sumner. "No known configuration. We have to treat it as hostile and prepare to attack-."

"No," Zelenka stated, smiling broadly. "I know this design. I helped to create it with Doctor McKay. It is a Daedalus-class 304 battleship. From Earth."

His words were met with stunned silence until Weir spoke up. "They came for us!"

"ETA?" Sumner asked, barely holding onto his usual gruffness.

"Five hours, forty-three minutes," Zelenka replied excitedly, and John had to admit that this was the best thing that had happened to them since before the storm.

"Let's roll out the red carpet," Weir stated, looking every bit as relieved and excited as everyone else gathered around the screen. With Atlantis low on power, still heavily flooded in areas, and tilting slightly after the storm, they had been in no position to defend themselves against any aggressor.

The Atlantis rumor mill kicked in at light speed and John could feel a buzz in the air wherever he walked. Even Atlantis seemed to be reacting to the news with the thrum in the back of his head seeming louder. Grabbing a mug of the Taranian drink that passed for coffee from the mess hall, he noticed the animated conversations going on all around him.

"Is it true?" The small Japanese scientist who worked with Zelenka had grasped the material of his jacket and he looked down at her and smiled.

"Yeah. It's an Earth ship." 

He kept any disquiet to himself, not wanting to stamp on the fragile hope building after months of enduring hardship following the storm. For all any of them knew this might not be a friendly ship despite its origins. From the briefings he'd had before stepping through to Atlantis, he knew Earth had enemies - in particular the Goa'uld - so this could easily be a Goa'uld controlled ship, looking to expand their control into Pegasus.

When he returned to the gate room a few minutes later, Weir was smiling widely.

"This is Doctor Elizabeth Weir of the Atlantis Expedition. Greetings from Pegasus, _Daedalus_."

She had put the call onto an open channel within the control room and John listened as pleasantries were exchanged. If Atlantis had been in better shape then the _Daedalus_ could have landed on the west pier but John suspected that her weight would be enough to tip Atlantis over at this point. Instead they had to wait until the _Daedalus_ moved into Geo-synchronous orbit above the city. John was about to mention using the gateships to ferry people between Atlantis and the orbiting ship when Colonel Caldwell spoke again.

"Permission to beam down, Doctor Weir."

Doctor Weir looked to Sumner, who nodded his agreement. She spoke with a strength of authority that had been missing these past months.

"Permission granted, Colonel."

A white light blazed on the gate room floor below and John blinked in surprise as several figures appeared and solidified. The light vanished leaving three jumpsuit-clad men and one woman, all of them looking around in awe, but Atlantis had that effect on people even in her current state. Doctor Weir moved quickly to the stairs, descending at a fast but elegant pace with Sumner, Kavanagh, Zelenka and John right behind her. Drawing up beside Sumner, John saluted to Caldwell but any polite and dignified introductions were lost as Zelenka noisily greeted the man standing beside Caldwell, hugging him fiercely while speaking rapidly in a mix of Czech and English. The other man seemed taken aback and patted Zelenka on the back but his eyes caught John's, head tilting and expression eloquently asking for an explanation.

Eventually Zelenka stood back and, in contrast, Kavanagh stood aloof, barely managing to acknowledge the new arrival except with a stiff nod.

Finally seeing the name on his jumpsuit - McKay - John understood Zelenka's excited greeting. This was his famed Rodney McKay, the miracle worker who would have had Atlantis dancing beneath his fingertips by now if he had been here instead of Kavanagh. Keeper of promises too, judging by the massive battle cruiser orbiting above their heads.

McKay frowned and John could see his critical eye going back over all that had previously held him in awe, seeing the signs of disrepair, and not just with the city but with those standing before him. He also leaned slightly, adjusting his stance a fraction.

"Is the city listing to one side?"

Zelenka pushed up his glasses. "There was storm damage - and a tsunami."

"Show me." He strode off towards the main staircase, followed by Zelenka.

"What do you think-?"

Weir cut off Kavanagh's angry words of protest. "Doctor McKay, welcome to Atlan-."

"Yes, yes. Busy now," he stated without breaking stride, waving a hand as if swatting away an annoying insect.

Hiding a smile, John spoke softly to Caldwell, who seemed un-fazed by McKay's attitude. "I'll keep an eye on him, sir." 

He left before Sumner and Caldwell could do more than nod, leaving a confused Weir and a spluttering Kavanagh behind. He caught up to McKay and Zelenka at the top of the main staircase in the control room, surprised that McKay was already tapping away on a laptop attached to one of the consoles. The main view screen came online and began to shift through schematics of the city, and John could swear the hum of Atlantis in the back of his mind had increased, as if the city was excited to see McKay.

John looked on in surprise as McKay accomplished more in a few minutes than Kavanagh had managed in their first month, guided by Zelenka only occasionally. Diagnostics were flowing across the screen and the two scientists paused now and then to point at different sections, sometimes agreeing, sometimes arguing. The argument got louder and more heated until Zelenka threw up his arms.

"Why did I pray you would come to Atlantis? I must have been delusional!"

McKay stared at him in shock, which rapidly turned to smugness. "You prayed for me?"

Zelenka stopped ranting and started to back pedal. "No. I did not say that."

"You said... I prayed you would come to Atlantis, which means you desperately needed me here."

"No. I did not-."

McKay waggled a finger. "Uh uh, you can't take it back now." He grinned, blue eyes sparkling with glee. "You needed me here," he sing-songed.

John laughed out loud, having not had this much fun in ages, and McKay turned on him.

"And what's so amusing, flyboy?"

Zelenka interrupted. "I would not insult the Major, Rodney, unless you like cold showers and quarters smelling of rotten cabbage. Atlantis likes him."

McKay opened his mouth to retort but John simply raised one eyebrow menacingly.

"Does that even work?" McKay pointed to John's face but, otherwise seemed less inclined to insult him so John gave him a smug grin, knowing McKay had answered his own question.

Zelenka snapped his fingers at McKay. "You must take Carson's gene therapy. It will turn you into light switch like Major Sheppard... if it takes."

"The ATA gene?"

"Yes. Sadly, it did not take for me or for Kavanagh, Doctor Weir and many others."

"Huh! Let's go."

John frowned. "Don't you want to check the city before-?"

"With the ATA gene, I can work even faster."

John was almost sure he felt a hum of approval inside his head from Atlantis, and he had to admit that he had instinctively known which of their people would have their ATA gene switched on before Beckett ever got a needle close to their skin. Atlantis seemed to recognize those that had the dormant gene, and he got that feeling from her about McKay. Within minutes he was watching as Beckett fussed around Rodney before preparing a syringe, making him roll up the sleeve of his standard-issue olive-green jumpsuit.

Beckett spouted lots of medical terminology about mice, retrovirus and genetic drift, and John smiled when it became obvious that McKay was tuning it all out as gibberish until he caught the words _side effects_.

"Side effects?"

"Dry mouth, headache... The irresistible urge to run in a small wheel." Beckett looked positively gleeful.

"Oh ha, ha." McKay winced a little as the needle pushed in, but Beckett was quick and surprisingly gentle, smiling back at McKay as he bent McKay's arm at the elbow afterwards.

"You should know in just a few hours... if it takes."

"It will," John stated, surprising himself by saying his thoughts out loud, and noticed Beckett giving him a slightly questioning, slightly knowing look. John wondered if Beckett, who was also a natural ATA gene carrier, had the same hum in the back of his head from Atlantis, and whether it let him know in advance who would be successfully ' _activated_ '. It had never occurred to him to speak to any of the other ATA carriers about it before now.

"Well," McKay stated. "I can't sit around here yapping all day. There's work to be done." He jumped off the side of the bed, swaying a little before frowning. He strode towards the door, hand waving over his head as Beckett yelled out, "You're welcome!"

John took a moment to exchange an exasperated but fond glance with Beckett, and then followed McKay and Zelenka, grinning widely.

Three hours later, the first Ancient machine begrudgingly lit up for McKay, and then there really was no stopping him.

****

Rodney couldn't believe the dire state of the city. As he went through the schematics with Radek, he could see the main problem areas and frowned because Radek was an excellent engineer. He could have figured out a way to pump water from some of those areas even if it had to be done manually. He said as much to Radek and saw his friend flush with embarrassment and anger.

"I do as much as I can to keep city afloat but Kavanagh is in charge. He says problem with the heating in the main control tower is more important than a listing city." Radek shrugged.

"The man's an imbecile."

"Yes. But what can one man do alone?"

"Install a ZPC for starters."

"ZPC?"

"Zero-Point Crystal." Rodney grinned at Radek's dumbfounded expression. "Admittedly, it's not as powerful as a ZPM but Jeannie's still working on that."

"You have made up with your sister?"

Rodney bristled a little. "I'm still barely on speaking terms with the English major who knocked her up."

"English major?" Sheppard had been eavesdropping.

"Not the kind you are undoubtedly thinking about, _Major_ ," he stressed. "He's a professor of Medieval Literature at the University of Toronto, not military." 

Rodney appraised the handsome major, wondering if he was all beauty and no brains like so many of the military that he'd had to deal with over the years, or if he had hidden depths like Yuri.

"-without the Leonov," Radek said, and Rodney blinked, momentarily confused until he realized Radek had been talking about the Mark IV, and not Yuri Leonov.

"Sorry?"

Radek sighed. "Perhaps if you could take eyes off pretty major for one minute, Rodney. Yes?"

Rodney rolled his eyes, a little annoyed at being outed to the _pretty major_ , and hoping the major wasn't the kind to take manly offense. Though, fortunately, the US military was a little more enlightened these days in allowing gays to serve openly, so there was far more tolerance. Glancing at Sheppard, he noted that rather than looking uncomfortable, Sheppard was at first a little startled and then possibly interested. Rodney turned away and smiled carefully. Perhaps the pretty major might offer the kind of diversion Rodney thoroughly enjoyed for when he wanted to slow down his brain at the end of a long day. Sex was an excellent stress reliever too, and great sex with a good looking man or woman - he wasn't too picky - made him the only kind of stupid he could tolerate, if only while that cocktail of sex hormones flooded his body. He'd also discovered that he came up with some of his better theories after great sex.

It was a win-win.

"Getting back to this... ZPC," Sheppard stated.

While they were talking they were also walking, and Rodney smiled as the door to the ZPM room opened at just a thought. He entered and glanced around, only to thin his lips in annoyance when Kavanagh stood up from where he was crouching behind the main console. Rodney stepped around and saw the three containers that he'd had beamed down from the _Daedalus_ only a few minutes earlier. Kavanagh had opened them and was turning one of the ZPCs over in his hands.

"In case you've forgotten, McKay, I'm in charge of the science teams on Atlantis."

"And in case _you've_ forgotten, Kavanagh, I am the only one in this room that knows how to integrate the ZPC with Ancient technology, so if you don't mind?"

He snapped his fingers at Kavanagh, aware that in a battle of wills, Kavanagh did not stand a chance against him. Taking an angry breath, Kavanagh shoved the ZPC into Rodney's hands and stalked away.

"Huh!" Rodney exclaimed before handing the ZPC over to Radek, who handled it far more gently - almost reverently. "These should give the city enough power to bring secondary systems back online and open a wormhole to Earth." He gave a lopsided-smile at Radek's stunned expression.

"You're like the gift that keeps on giving, aren't you?" Sheppard stated, and Rodney grinned.

Forty minutes later, the lights in the city visibly brightened, and Radek answered a call on his radio.

"Yes, Doctor Weir. We have power once more."

****

Two hours later, John dragged both McKay and Zelenka towards the conference room at Weir's order. As they walked towards the room, the two scientists exchanged ideas and finished off each other's sentences the whole way, finally ending with Zelenka saying, "If I was not straight then I would kiss you... or punch you. I am still undecided."

John knew that feeling. McKay was arrogant, rude, and petty at times, but he was also funny, insanely brilliant, and very easy on the eyes. He would be a terrible poker player as his face showed every emotion instantly, from the slant of his kissable lips to the twinkling in his expressive blue eyes. He seemed incapable of subterfuge, which John knew was highly unlikely as not even a scientist of McKay's brilliance would be brought into the Stargate program if he had problems keeping secrets. It was too big a risk.

No. It was more likely that McKay simply chose which secrets were worth holding onto at any given time.

The conference room was already full but someone had left three seats clear, obviously intended for them. McKay took the seat between Caldwell and the other guy who had beamed down with them, whose name John had barely caught - Woolsey? Given a choice of seat by Kavanagh or Sumner, Zelenka sat down next to Kavanagh leaving John the seat by his C.O. As soon as he was seated, Weir called a start to the meeting. Each department was represented at Kavanagh's insistence and spoke up in alphabetical order. They were barely through the departments starting with the letter B, listening to Doctor Parrish describe the trials and tribulations - mostly trials - of Botany on Atlantis, when McKay spoke up.

"Is this really necessary?"

Kavanagh folded his arms, mirroring McKay. "As Chief of Science on Atlantis, I felt it relevant for this meeting to see our accomplishments."

"Accomplishments? Doctor Church..." McKay waved a hand at Parrish, "...has revealed a sad lack in accomplishments due to problems within the hydroponics area. Before him, Doctor Biochemistry here," he waved at a young woman standing against the wall, "...mentioned a lack of suitable laboratory space, and Anthropology is still awaiting access to the Ancient database. Hardly a glowing stack of accomplishments."

Weir stepped in before Kavanagh could respond, leaning forward. "And how would you prefer to proceed, Doctor McKay?"

McKay looked across the table to Zelenka before turning back to Weir. "How about these people send in a report of all the problems in their respective areas and then, instead of wasting my precious time now, we spend this meeting talking solutions to far bigger problems. Oh, such as a slowly sinking city."

"It's listing," Kavanagh exclaimed.

"It's sinking," McKay came back, and gave Zelenka a hard stare, obviously expecting Zelenka to support him.

Zelenka nodded, pushing his glasses up his nose nervously. "Rodney is correct. The city is still taking on water. With each passing day, the rate increases. Eventually it will reach a critical tipping point."

"Yes, in two years! That hardly warrants us panicking now, McKay." Kavanagh jerked his chin up.

"And if there's another storm? Or the city springs another leak due to the increasing pressure of water in areas that were never meant to be underwater...?" McKay trailed off with a sardonic smile, not really needing to spell out how calamitous that would be to all of them.

"And what are you suggesting, Doctor?" Sumner asked.

"I have a-."

"We."

McKay grimaced. "WE have a plan." He looked to Caldwell. "But it will require the use of the _Daedalus_ , or more specifically, the Asgard beaming technology." He turned to Weir. "Your gateships." He turned once more to Sumner. "And your underwater engineers."

"Go on," Caldwell ordered, and John had to admit that McKay and Zelenka's idea - likely formulated when John left them for half an hour to have lunch while he attended to his duties elsewhere - was crazy yet simple and elegant.

McKay intended to beam large metal plates, cut from towers that were already beyond repair, into the flooded compartments where the outside layer of Atlantis had decayed or otherwise ruptured during the storm - or during the ten thousand years while the city rested at the bottom on the Lantean ocean with its shield slowly collapsing. The gateship would help maneuver the plate into place from the outside while divers welded the plate to Atlantis, sealing the compartment. The _Daedalus_ would then beam out the divers and the water could then slowly be pumped out of the area.

Kavanagh sniffed. "Obviously I would have come up with a similar solution if I'd had access to beaming technology." McKay raised both eyebrows but fortunately chose to ignore Kavanagh. "Of course, I will oversee the work," Kavanagh added, and John saw McKay grind his teeth in annoyance but it was Kavanagh's prerogative as head of science in the city. McKay would have to take a back seat while Kavanagh took all the credit if this was successful.

Woolsey spoke up for the first time. "Unfortunately, Doctor Kavanagh, you and several other senior staff are expected back on Earth for a debriefing now Doctor McKay has finished installing the ZPCs."

Everyone looked to McKay, whose earlier annoyance had evaporated and who was now sporting a smug grin. "ZPCs are in place. You can dial home whenever you're ready."

Weir nodded and looked around the room. "This would be the perfect time to inform you of temporary staff changes. Doctor Cole will head up medical in Doctor Beckett's absence, Major Sheppard will be the temporary military commander, Doctor Zelenka will head up sciences, and I.O.A. Representative Richard Woolsey will take over in my absence. We can be ready to leave for Earth in two hours if no one has any objections." He glanced around the conference room. "Any questions?"

Zelenka raised a hand awkwardly. "Yes. I am happy to step aside and allow Doctor McKay to head up sciences in Doctor Kavanagh's absence." He talked over Kavanagh's protest and glanced across at Caldwell. "If you are willing to spare him."

Caldwell straightened. "Doctor McKay is not an official member of the _Daedalus_ crew. He is on board purely to supervise the maiden intergalactic flight of the ship. If he wishes to take up this assignment for the duration of our stay on Atlantis, then I will not prevent him from doing so."

Weir looked at McKay with intrigue. "Doctor McKay?"

"Obviously, I would be the best man for the job," he replied arrogantly but John saw the small acknowledgment towards Zelenka.

"Well, with all this settled... meeting adjourned." Weir smiled and stood up.

Before anyone could turn towards the door, McKay spoke out. "I want those reports in three hours, people. Use bullet points unless you want me to fall asleep reading it."

John saw various nods and verbal acknowledgments as the room slowly emptied, leaving only McKay, Zelenka and him. He waited until McKay was about to stand.

"I've got a question for you. Why didn't the SGC dial Atlantis from Earth using those ZPCs of yours?"

McKay smiled and sat back in his seat. "So there are some brains beneath that unruly mop of hair."

"Hey!" John patted his hair. "Enough with the hair, McKay. At least I have some."

McKay twitched so his receding hairline was obviously a sore point with him.

"The reason why the SGC cannot dial in is because I haven't installed the ZPCs. Unlike here, it would require weeks to build the necessary housing unit for the ZPCs and then rewrite the gate protocols to use them."

"You didn't need to do any of that here," John pointed out.

"That's because this is an Ancient technology rather than bastardized human and Goa'uld technology." He sighed. "Jeannie's working on it."

"Your sister."

"Yes."

"Is she better than you?" he asked, enjoying teasing McKay.

McKay bristled. "Swings and roundabouts, Sheppard. She's better at some things, I'm better at others."

John was impressed as he could see how hard that was for McKay to admit. "And what things are _you_ better at?" John purred almost seductively, enjoying the little flirtation even more when McKay's cheeks flushed a pale pink and his pupils dilated.

A snap of a laptop lid brought his eyes to Zelenka, and John blushed at forgetting the other man was there.

"If you two have finished flirting, then we have work to do."

"Right. Yes." McKay stood up and Zelenka followed, and John smiled knowingly when McKay glanced back before the door closed behind him and Zelenka.

Slouching back in his seat, John's lips quirked up a little more just from knowing McKay - Rodney - was interested in him. It had been a number of years since he last considered taking a male lover but he was thinking about it now. Even the lifting of restrictions on serving gays, just before the start of the Atlantis expedition, had not really affected him. There were several guys on Atlantis who had shown interest in him, even openly flirting, but none of them had caught his eye in return, not even for a little stress relief. He'd turned down even more offers from women, and because of that he had heard rumors spreading that he was asexual. Admittedly, he was bisexual, though if he had to state a preference then it would be other guys, but that had not stopped him from enjoying the company of women - and even marrying Nancy just to appease his father.

If John had a physical type then Rodney would be it. He had never gone for the overtly hairy, athletic or muscle-bound guys, nor for the wilting flower types and stereotypical gays. He liked broad shoulders, strong arms, competent hands, just enough extra padding to get a good grip, and a nicely curved ass. That Rodney also had incredible blue eyes and such a mobile mouth was the cherry on top. Yet what had drawn him to Rodney when there had been a few others of his type that John had shied away from over the years, was the quirky personality and intelligence.

He liked men with brains. He liked seeing all that amazing intellect turn to mush as he fucked their brains out; liked driving them to incoherence until all they could see and smell and feel was him. It was his biggest turn-on - his personal kink.

From what he'd already seen of Rodney, he knew he wouldn't have to work too hard to get him into his bed. With that in mind, John pushed up and walked from the conference room. He was already doing most of Sumner's paperwork as well as working out the duty rosters for the marines so there wasn't a lot for Sumner to hand over, but he figured he ought to at least check in with Sumner before the Colonel left for Earth. Afterwards, though, he had far more personal plans to put in place; plans that involved Rodney McKay.

****

Rodney was starting to wonder if he was a masochist for taking on so much at once but he had never been work shy. He'd always loved the challenges in any scientific situation and this was just another of them. An hour earlier, he had stood on the balcony above the gate room and watched as Sumner and Doctors Weir, Beckett and Kavanagh went through the gate along with a few others who had asked to go home. They would be gone for at least two weeks, perhaps three if they decided to take some personal time as well. Of the four command personnel he would only miss Carson Beckett as he knew an outpost this far from Earth could never have enough medical doctors, especially talented ones like Carson. No doubt Doctor Weir and Colonel Sumner were good at their respective jobs but he didn't really know either of them - and the less said about Kavanagh, the better, in his opinion.

Kavanagh should have stuck to biometrics, where he was actually useful.

As he took a moment to read through the first of the reports, part of him wondered what Kavanagh had been doing here for the past year, seeing Radek's handiwork in most of the repairs around the city. Unfortunately for Atlantis, Radek was only one man with limited influence over the other science sections. He suspected Radek had tired of trying to get more resources out of Kavanagh and had simply done as much as he could.

As chief of science, albeit temporarily, Rodney had the power to utilize any science resource within the city - and even to ask for military assistance with the city repairs. Rodney might refer to them as grunts and idiots on occasion but he did appreciate their abilities for the most part - but then most people were idiots in his eyes, unable to keep up with his thought processes.

It was likely that Kavanagh had never even considered that the military would have picked men for the expedition with skills that went beyond pointing a gun and shooting. According to the expedition files that Rodney had read from cover to cover on the journey to Atlantis, the military on Atlantis had many highly skilled personnel. They had structural engineers and explosive and ordnance experts, with the skills required to repair weapons and make ammunition. They had electrical engineers, geologists, computer technicians, and a variety of other skills that might seem unimportant on their own but were just as essential on a one-way trip to another galaxy, such as a quartermaster, and several cooks with biochemistry degrees. Even pretty flyboys like Sheppard were essential for moving supplies and people, as well as providing air support.

As far as Rodney was concerned, the military was an untapped resource and he said as much to Radek.

"I mentioned this to Kavanagh but he insisted that we had sufficient of our own scientists to cover all necessary work."

"The man's an idiot," Rodney mumbled around a sandwich that he'd ordered one of his new people to bring up to him. Doctor Habitat - or something like that - had seemed a little put out having to carry out such a menial task but Rodney was certain he'd be grateful when some of the items on his department's wish list were actioned.

Captain Vega entered and glanced at him warily. "Major Sheppard ordered me to report to you, sir."

"Ah yes. Captain Vega. I have an assignment for you." He motioned towards a seat.

Aware that the _Daedalus_ could be recalled to Earth at any moment, Rodney did not want to miss the opportunity to use her beaming technology to help plug the worst of the holes. Therefore, the work had to take precedence over all the other reports that were already flooding in from various departments.

In the next hour he and Radek set up the schedule for repairing the damaged external walls of the city with Captain Vega, having assigned her the task of overseeing the structural repairs with Sheppard's permission. Vega had arrived on the _Daedalus_ with him and Rodney knew she was more than capable of handling the task. She had grown up helping her father in his marine salvage business before spending several years training in land search and rescue with the military. As one of the first US response teams on the ground following a major earthquake in Central America, she had earned her coveted reassignment to the SGC on her merits and professionalism as both an engineer and a soldier.

He tapped his radio in response to a call. "Yes. We're on our way." Looking across at Radek and Vega, he smiled. "Looks like they're ready for us."

"I will oversee things from up here," Zelenka stated.

"Really? Because part of this is your idea and I would have thought-."

"No. Seriously, Rodney, I would prefer not to sit in tiny tin can beneath surface of the water."

Rodney grimaced, suddenly feeling his own claustrophobia close in on him. He swallowed hard and headed out with reluctance with Vega following, recalling the tiny quarters on the _Daedalus_ and how hard it had been to stay in them, even to sleep. He was surprised to discover the gateship cockpit was a little more spacious than his imagination had allowed. He was also surprised to see Sheppard in the pilot's seat. Sheppard gave a general wave of his hand towards the copilot seat, but Vega chose to take the seat behind Sheppard, leaving the copilot seat free for Rodney. When Rodney glanced inquiringly at her, she gave him a one-shoulder shrug.

"I don't have the gene, sir."

"Does that matter?"

Vega ignored him, leaving Rodney wondering at the relevance of her words as it really didn't matter whether she had the gene or not; Sheppard was piloting. It occurred to him that maybe she didn't want to sit next to her new C.O. this first time through the repair process. Or maybe she simply wanted to concentrate on coordinating the teams rather than glancing into the murkiness beneath the city. Coming from a marine salvage background, she was probably already bored with the view.

When he looked to Sheppard for an answer, all he saw was a smirk. "Sit back and enjoy the ride, McKay. Captain Vega will have plenty of opportunities to take the copilot seat."

Since having the gene therapy, Rodney had felt a tingling sensation at the back of his mind and he knew it was a neural or telepathic interface with the Ancient technology. He felt that hum grow stronger now and blinked as his thoughts for the upcoming repair task brought images up onto the front view screen.

"Huh!" Deciding not to waste an opportunity, he focused on the display as he went back over the plan with Vega. He noticed one small flaw in the plan and corrected it before a different sense - his sixth sense - kicked in to tell him that he was being watched. Looking across to the pilot's seat, he found Sheppard smiling softly at him.

"You've picked up the mental component really fast. I still have to cajole Beckett into operating even the simplest equipment, unless it's medical."

Rodney preened at the unexpected praise but quickly turned his attention back to the task at hand when Sheppard took the gateship up. When they didn't submerge immediately, Rodney looked up from his datapad to see the whole of Atlantis spread out before him - and she was beautiful. Sheppard weaved them between the towers. For once Rodney decided not to analyze but to do as Sheppard said, and simply enjoy the ride. Eventually they headed down and slipped gently beneath the waves lapping against the city, quickly moving into the murky depths.

Sheppard glanced towards Rodney briefly. "We never realized the gateships could go underwater until you mentioned using them this way. Seems kind of obvious now."

"Wait. Does this mean this is your first time piloting underwater?"

Sheppard shrugged with one shoulder and Rodney felt the walls close in on him once more. He closed his eyes.

"Blue skies. Wide open spaces," he murmured under his breath in a quiet mantra.

"We're here," Sheppard stated with what sounded like laughter in his voice, and Rodney pushed the panic aside so he could concentrate.

By rights Rodney didn't need to be down here under the water at all but he had never been one to sit back and watch from the sidelines. He needed to see everything in operation this first time through, to ensure he hadn't overlooked a vital task. Vega seemed very confident though and he listened in on the radio as she coordinated the diving teams, making certain they were ready to proceed.

The engineers were already cutting the first plate from one of the more severely damaged towers out near the east pier.

Rodney ordered Hermiod to send down the plate as soon as the engineers were ready, watching as it materialized exactly where it was needed. Divers outside attached cabling to ready-made hooks and then to the gateship, and Sheppard eased back until he was holding the plate firmly in place across the largest hole beneath the waterline. He heard Hermiod confirm that the divers were in position and initially saw a few flashes as they started to weld the plate into place. He knew this was more of a band aid than a full repair but once the water was pumped out, and with the shield powered by the ZPCs, there would be a greater chance of making a permanent repair. 

An hour later, they were ready for the next plate with a new set of divers ready to go. Altogether they needed to weld eighteen more plates in decreasing size before they could re-float the city properly. Adhering strictly to safety protocols, it would take more than a week but Rodney could see that Captain Vega was capable of supervising the repairs without him micro managing her and her teams, which was joint military and science.

"Captain, I expect daily reports on progress and immediate notice if you run into any problems."

Vega raised her eyes, glancing across at Sheppard, who merely shrugged, before answering. "Yes, sir."

"Hermiod. Lock onto my subcutaneous transmitter and beam me up."

Moments later, the inside of the gateship disappeared, replaced by the inside of the transportation room. He felt a moment of displacement that had nothing to do with the beaming, and was about to request an immediate beam down to Atlantis when the door opened and Caldwell stepped in.

"Doctor? Any problems?"

"On the contrary, it went extremely well, if I do say so myself."

Caldwell nodded. "Then I'll let you get back to Atlantis."

"Yes. Yes. Lots to do."

Caldwell nodded towards the transporter operator and moments later the beautiful architecture of Atlantis formed around him. The hum that had been strangely muted while on the _Daedalus_ came back full strength, making him realize why he had felt a little unsettled earlier. He pushed the thought from his mind when he saw Radek waiting for him, quickly moving up the stairs to join him.

Moments later they were deep in discussion as they looked through the reports that he'd requested at the meeting. Fortunately, most of the department heads had listened and had presented the reports with a bullet point list of requirements in priority order. It made it easier to see where the problems lay, though Rodney was amazed by some of the requests that were so minor in nature that they would take him only minutes to fix. Admittedly, it might take someone else a little longer but no more than an hour.

"Kavanagh saw these problems as nonessential, and I am only one man," Radek explained.

As they had gone through the reports, Rodney had created a new document to organize the requirements and problems into specialist areas - technical, construction, material requirements, etc. They broke the new list down even further and Radek, gleefully, fired off emails to specific areas with the work requests.

Setting up new laboratory space would have to wait until after the construction teams had completed the major repairs on Atlantis to make her water tight once more. Other requirements could be sent back to Earth. Hopefully, once the Stargate was operational in both directions, receiving fresh supplies of equipment, materials, and people would resolve some of the other issues. Even so, Rodney knew it would be better to become self-sufficient rather than rely solely on Earth. The Goa'uld were still problematic, and there had been rumors of another race of beings called the Ori who wanted to control the Milky Way and all the humans in it. He didn't know a lot about them, overhearing snippets of conversations while at the SGC, but it didn't sound good.

By now it was getting very late and he was starving, so he made his way to the mess hall, hoping they were serving something citrus-free. For once he was in luck, with the server insisting that there was no citrus in the meatloaf. He made his way to a free table with an excellent view of the city beyond, and sat down. Picking up his knife and fork, he'd barely managed one mouthful before a tray slid into his view on the opposite side of the table. Looking up he was surprised to see Sheppard, and took a moment to quickly glance around, assuming all the other tables had filled up suddenly, but the place was still fairly empty. It meant Sheppard had chosen to sit with him when, usually, people tended to stay as far away as possible. Narrowing his eyes, he stared at the major.

"Is there a problem?"

"Nope." Sheppard dug into his meatloaf, taking a few bites before casually asking, "So how was your day?"

Confused, as he was so unused to small talk, Rodney looked around for a hidden camera, wondering if it was a trick question. In the end he realized Sheppard was actually waiting for a response and he looked around again, this time in hope that the answer would appear out of thin air like magic.

"It's not a trick question... Rodney." He took another mouthful, chewing and swallowing before continuing. "My day was pretty good. I spent it mostly underwater piloting a gateship. We managed to get another section repaired before we called it a day."

"Yes, I know. Captain Vega kept me apprised of your progress."

"So... What have you been up to?"

"Cleaning up Kavanagh's mess," he replied, and that seemed to open the floodgates as he described some of the petty tasks Kavanagh had left to fester alongside the more dangerous and important stuff. It wasn't that Kavanagh was unintelligent but he was simply too pedantic, wanting to cross every T and dot every I before committing to anything outside his control. Working on the Daedalus project, Rodney had learned how to take a step back and allow his team to take on certain tasks without him micro-managing. It had been tough at first as he was used to doing everything himself, and there were a few times when he regretted handing a task to certain individuals, who had proved totally incompetent.

It took Rodney a while to realize that Sheppard was actually goading him on in his rant, interjecting now and then with small remarks just to keep him talking. He stopped and glared when he realized the ranting had moved from work to movies, not sure when or how that happened, or if he was being mocked.

"Seriously? You liked _Back to the Future_?"

Sheppard sipped at his coffee and shrugged. "It's zany... and it's a DeLorean, with a flux capacitor."

Rodney wasn't sure whether to be horrified or not, deciding that Sheppard had to be deranged, and yet there was something so appealing about his delusion that it was a good movie. Or maybe it was the boyish good looks, the mussed hair, and the look in his eye that made it obvious even to Rodney that the guy was flirting with him - badly.

"Maybe I can show you the merits of that movie?"

Rodney blinked in surprise, recognizing the variation of the _Come back to my place and I'll show you my etchings_ chat-up line. He grinned. Sheppard was really bad at this, but then Rodney knew his own pick-up skills were infinitely worse. And what was the worst that could happen? That he could go to Sheppard's quarters and end up spending an evening watching a terrible movie in gorgeous company? It was worth the risk so he nodded.

"Fine. Lead on."

They bused their trays and left the mess hall, heading towards the transporter. A quick glance showed Sheppard licking his lower lip - just a flash of tongue - but along with the slightly heightened color and the way he was snatching quick glances back at Rodney in turn, Rodney knew he wasn't mistaken about Sheppard's interest in more than just a terrible movie.

When they reached Sheppard's quarters, closing and locking the door behind them, Sheppard seemed far less confident, rubbing the back of his neck in a nervous gesture. Rodney took a moment to take in the room, noting the Johnny Cash poster above the bed and a framed photo of a small kid with... was that Evel Knievel? Otherwise the room looked Spartan, bereft of any personal touches.

If Yuri had taught him one thing during their short time together, it was how to bluster through these awkward moments. He stepped into Sheppard's personal space, reached up to cup his face in one hand, leaned up slightly and kissed him. Sheppard froze for a moment, as if he truly hadn't seen that coming despite being the one to bring them here. It lasted but a moment though before his lips softened and his hands were reaching for Rodney - one around his waist to draw him closer and the other cupping the back of his head to stop him from pulling back from the kiss.

The kiss deepened, and Rodney moaned in approval. When they broke for air, Rodney stepped back just a fraction, enough to give him room to unzip his jumpsuit. Shrugging out of the top half and leaving it hanging from his waist, he grabbed the hem of his t-shirt. It came over his head easily as Sheppard took over, stripping it from him and discarding the t-shirt somewhere on the floor. Rodney reached for Sheppard's black t-shirt, eager to have them both half naked, but Sheppard's hands were gliding up Rodney's sides, the callused pads of his thumbs finding Rodney's nipples and rubbing over them, sending shock waves of pleasure through him. He'd always been so sensitive there and Yuri had taken that sensitivity to an art form; his eyes closed in the rush of pleasure through his body as John played with him beautifully.

"Sheppard," he gasped, now achingly hard and needy.

"John. It's John."

Before Rodney could respond, John was kissing him again, no longer shy and awkward. Their mouths slid apart and Rodney tilted his head as John licked and kissed and bit the side of his throat. And all the while, those thumbs played with him. With a gasp, Rodney pulled back a fraction, desperate to feel John's naked skin too. This time he shoved at the black t-shirt, and John took the hint, dragging it over his head quickly. Rodney's fingers carded through the soft dark curls on John's chest, unerringly finding one tiny nipple within the thick chest hair and tweaking it hard enough to gain a gasp from John. With a sound that was almost a growl, John plundered his mouth in another hard kiss while his hands worked at lowering the zip of Rodney's jumpsuit the rest of the way down until it dropped around his ankles, before pressing the palm of his hand hard against Rodney's cock, rubbing up and down in delicious torment, skin separated only by Rodney's thin cotton boxers.

Rodney managed to pull back as his climax was building, barely avoiding the indignity of coming in his boxers. He kept John at arm's length as he regained control, stepping back awkwardly and sitting down on the bed. He toed off his shoes and socks before kicking off his jumpsuit. When he looked up, John was watching him avidly, lips swollen and red from kissing and eyes glittering in desire. Slowly, John began to strip too, but a devilish look crossed his face once he was down to just his boxers. He stepped forward, between Rodney's legs and rested one hand on Rodney's head, stroking through his hair before gently pushing his head down towards the thick cock tenting his boxers.

Rodney needed no other invitation. He tugged at the waistband enough to free John's cock, wrapping the base in his hand and leaning forward to lap at the pearl of precome beading on its head. John moaned as Rodney licked along the length of the hard flesh, tongue teasing the slit, pushing against the sensitive bundle of nerves beneath before opening his mouth and taking John in. He sank down onto the thick cock, letting his teeth scrape very gently over delicate, soft skin before setting up a rhythm with hand and tongue and mouth. He could feel John's hand tightening in his hair, see the muscular thighs tighten against the need to thrust deep and hard, letting Rodney set the pace. Rodney could feel John losing the battle, glancing up to see John's head throw back and body arch as the first bitter jet of come coated Rodney's tongue. He swallowed quickly, taking it all, wanting every last drop until John was curling back over him with legs shaking from the power of his climax, hands heavy on Rodney's shoulders for support and balance.

Letting go with an obscene slurp, Rodney maneuvered John to the bed before standing up. Slowly he removed his own boxers before pulling John's the rest of the way off him. By now he was desperate for his own release so he lay along the length of John, one leg thrown over John's to offer better friction as he thrust against John's thigh and hip, closing his eyes as his climax swept over him quickly, splattering come over John's sweat-slicked skin. He collapsed partially on John's chest, cheek brushing against soft curls matted with clean sweat. Inhaling, Rodney sighed, having forgotten how much he loved the pungent scent of male sex and sweat.

"Fuck, that was good," he murmured and, beneath his head, he felt John's chest rise and fall rapidly as he laughed softly.

"Yeah. That was good."

They drifted for a time in post-coital lethargy but eventually the stickiness of sweat and come had Rodney moaning in irritation. He clambered out of the bed and headed for the bathroom, pleased to find decent washing facilities. The pad of bare feet behind him make him glance over his shoulder, and he jumped a little as John grabbed one ass cheek and kneaded the flesh.

"Next time I want this, " John murmured before stepping past and starting up the shower.

"Next time I might let you."

Clean and dry, they crawled back into John's terribly small bed, with Rodney's head using John's shoulder for a pillow, and slept.

****

Rodney was gone by the time John woke, and in his place was a note scrawled with, ' _Get a bigger bed. Preferably before tonight. MRM_ '. Idly scratching at his chest, he grinned as he thought back to last night - and to that talented mouth. It had been a long time since anyone had made him feel this good and he stretched out like a cat, enjoying the loose limbed feeling of having had really great sex.

Better still was knowing Rodney didn't consider it a one-night stand, and had given him a wicked smile when John told him that he wanted his ass next time. Still feeling buzzed with pleasure, he jumped out of bed, going through his morning routine before firing up his laptop to check his emails.

There was nothing too important waiting for him so he fired off one to Sergeant Temu, their quartermaster, asking him to find a larger bed for his quarters. John wondered how long it would take before the rumors spread around the city - if they hadn't already started after he disappeared with Rodney late last night. He knew no one under his command would care that he'd bedded another guy because the SGC had no room for the narrow-minded among its ranks, not when it was regularly dealing with alien customs and situations. The SGC had the pick of all the military services, and could afford to weed out the homophobes and bigots. It didn't stop hardened soldiers like Sumner and Bates from seeing every outside contact as a potential threat situation, but that was just part of the military mindset rather than actual prejudice. Even John tread carefully when dealing with non-Lanteans, but he'd learned from a young age how to schmooze with the best of them. His father had expected it of both him and his brother, grooming them to take over the family empire before John scuppered his father's plans for him by joining the US Air Force.

He had never regretted that decision. 

Leaving his quarters, he made his way to the mess hall via the control room, taking a moment to check in with the gate technician and his temporary 2IC first. Major Lorne was fresh off the _Daedalus_ but was also a natural ATA gene carrier, and he seemed personable enough. John outranked him only in seniority but it was enough to make him the highest ranking officer in the city, if he didn't include Colonel Caldwell. Caldwell seemed happy enough to command Earth's new flagship battle cruiser though.

The mess hall was crowded but there was no sign of Rodney or Zelenka. However, he did see Captain Vega and some of her crew seated around a table discussing plans for the coming day. He considered joining them but then decided to let her finish formulating her plans before he went across as he knew from experience that there was nothing worse than having your C.O. breathing down your neck while you tried to work.

It was bad enough that he was currently one of only three pilots on Atlantis with the skill to control the gateship in the turbulent undercurrents beneath the city - though he hoped Lorne would prove a good pilot once he was trained. All the teams were taking the work in shifts due to the concentration needed, wanting to ensure no one made any costly or potentially fatal mistakes. At least they had a safety net while the _Daedalus_ was in orbit, with Hermiod monitoring the teams and prepared to beam out anyone in difficulty. It was a safety precaution that Rodney had insisted upon before handing over the reins to Vega.

John's duty shift as a pilot started as soon as Vega was ready to proceed.

He looked up from his reconstituted scrambled egg on toast as a shadow fell over him.

"Captain Vega."

"Sir, we are ready to head back out when you are."

"Give me a few minutes to finish up here and then I'll meet you in the gateship bay."

"Yes, sir."

Twenty minutes later his gateship was sliding beneath the waves and heading towards the next section of Atlantis that needed repairs. An hour passed by in a blur as he battled the currents to keep the last of the really large plates of metal in place while the divers welded it to Atlantis. From here onwards, the plates would be smaller, requiring only minimal assistance from the _Daedalus_ in transporting them. There was still plenty of work ahead of them though, with smaller fractures to weld once the eighteen major holes were sealed.

Another forty minutes passed before he could surface, and John headed straight for the gateship bay, setting her down and accepting a word of thanks from Vega before exiting. He decided to grab a coffee from the mess hall before heading to his small, out-of-the-way office, intending to spend a few hours going through the emails and reports that seemed to have tripled since Rodney took over as Chief of Science.

There was still no sign of Rodney but John noticed greater activity in the mess hall than usual, with people seated in groups, talking louder and more animatedly while huddled around laptops and papers. He saw Lorne and caught his attention.

"What's going on?" he nodded towards the closest set of scientists.

"McKay's got all the scientists stirred up."

"Yeah?"

"He's reassigned work loads and even requisitioned a few more of our men to help with technical and mechanical issues. Corporal Singh is installing software onto laptops as we speak, and Palmer is fixing a short in the electrical system that's stopping the botanists from powering up their special plant-growing lamps."

"I see."

"A few of the scientists are not too pleased with the new management style, and I'm surprised no one has tried to shoot McKay... yet."

John smiled. To be honest, the science area had needed a shake-up to overcome the apathy that many had fallen into when their work was not considered high enough priority to warrant technical or other assistance. He knew the botanists, in particular, were fed up of not being allowed to go off world to see other planet's flora. Some had never even stepped off of Atlantis onto the mainland, and there was only so much they could do with the desiccated remains of ten thousand year old plants littering some public areas in the city.

"So where's McKay now?"

"Last I heard he and Zelenka were in the main engineering lab, building something to pump out the water from the submerged parts of the city, powered by one of the Leonovs."

John nodded. "So what other resources has he requested?"

Lorne took the hint and accompanied him back to his small office, and between them they went through dozens of emails, reorganizing duty rosters to free up some of the technical experts among the military. One of the requests was for Sergeant Chuck Campbell to take over the gate technician duties permanently, freeing up the expedition's linguistics specialist, Doctor Huang, to work on a better translation interface for the Ancient database.

Between them, they made their recommendations, not allowing Rodney to have his own way in every instance but seeing no reason not to reassign some of the military to cover strategic roles such as gate technician. Campbell was perfectly suited to the task. Two hours later, they managed to reach the end of the current stream of emails from Rodney. Another email popped up as he moved to close his laptop but this one was from Sergeant Temu. He opened it without thinking, only to tense when Lorne read it out loud.

"Bigger bed located and moved into your quarters."

John shrugged, trying not to look embarrassed. "I think my quarters once belonged to a kid," he stated, hoping Lorne wouldn't question him further.

Lorne barely kept a smile in check and stood up. "If that's it for now, sir, I should start passing out the new duty assignments."

"Sure. Go ahead."

He dropped his head to the desk as soon as Lorne closed the door on his way out, wondering if Lorne was now having second thoughts about being John's 2IC. But then he smiled as he remembered last night, and his plans for tonight. As much as he had liked the feel of Rodney lying heavy and sated half across him in the narrow bed, he wanted to have the extra space for more adventurous sex, without fear of tumbling off the side and spraining something important.

If tonight turned out even half as good as last night then it was worth a little embarrassment on his part. And anyway, Rodney was well worth it.

****

This set the pattern for the rest of the week, with John helping with the repair crews, performing his own duties, and meeting Rodney later in the evening for dinner before they headed back to John's quarters and that big, new bed. The week stretched into another and John realized he had never felt so good in his life.

He loved the way Rodney had turned the whole of Atlantis upside down. Most of the city called him arrogant, petty, and obnoxious as he ripped their theories to shreds and called them imbeciles, but none could dispute his sheer brilliance or the fact that every department was showing increased productivity since his arrival.

John saw a different side to Rodney. He enjoyed his wicked sense of humor and surprising naiveté, loving how easy it was to fluster Rodney, teasing him both in and out of bed. The only problem was it couldn't last. Jeannie Miller had integrated the ZPC with the SGC's systems, and the first person to step back through was Carson Beckett. John knew it was only a matter of time before Kavanagh followed, and then Rodney would be gone.

With the Stargate now operating in both directions, Caldwell had received orders to head back to the Milky Way with the _Daedalus_ within two days, and even though Rodney could choose not to go with her, John knew that he would. Rodney had designed and built her, and as they lay side by side on the bed, loose-limbed with sated pleasure, he heard Rodney sigh.

"I'm leaving with the _Daedalus_."

"Why?"

"Because I know her better than anyone, human or Asgard. I need to see her back to Earth then go over all the data from the mission. Engineering diagnostics, hull integrity, intergalactic drive and even the Asgard beaming technology. I need to make final recommendations and adjustments before they complete construction on the next ship."

"How long will that take?"

"Maybe a month. Less if I still have my team back on Earth and don't get handed any idiots to re-train."

John smiled wryly but continued looking up at the ceiling as Rodney shifted beside him.

"Look, Sheppard... John. I've... This has been really good and I-." He huffed in annoyance. "I'm going to miss this... Us. I'm going to miss you."

John rolled his head to face Rodney, finding him leaning up on one elbow and looking down at John. He looked as miserable as John felt, with his mouth tilted down in one corner and his blue eyes sad.

"I'm gonna miss you too, buddy."

"Yes. Well. I don't leave until after tomorrow so maybe we can make a few memorable last nights. Wake early and-."

John rolled over and pinned Rodney to the bed, kissing him soundly even though there was no chance either of them was going to get a rise out it so soon. He just wanted to feel Rodney pressed up against him; the silken feel of his skin, the soft hair and the heat that Rodney gave off like a furnace, especially when they had sex. They kissed sloppily, almost playfully until Rodney yawned widely.

"Am I keeping you awake, McKay?"

"Sorry! Sorry. I'm so tired."

John pulled at Rodney until they were both settled comfortably before dragging the light cover up over them. He mentally commanded the lights to lower until the only illumination was from one of the two moons that had risen earlier. He had plans for when they woke tomorrow, wanting to make sure Rodney thought about him every time he sat down for a week.

With that last, hungry thought sending small echoes of pleasure through him, John dropped into sleep with Rodney half-draped over him, hot and heavy in his arms.

**** 

Rodney woke early the following morning, and took a moment to enjoy watching the man sleeping in the bed beside him. Meeting John was an unexpected pleasure, but he couldn't help making comparison's between John and Yuri. Both were tall and dark haired, both were very easy on the eye... and both were military. Unlike most of his relationships with women, both men had stuck with him beyond a one-night stand, finding pleasure in his company. For some unknown reason, he always managed to say or do something to upset women, usually ending in them either slapping him round the face, or destroying some possession of his - like shredding his clothes, in one memorable instance.

With Yuri it had been different. He had accepted every unintended insult with Russian stoicism, and found a pleasurable way to make Rodney pay for the indiscretion later. He had seemed to know that Rodney wasn't being deliberately rude or cruel to him when they argued over his work and security. John was the same. He seemed to accept Rodney's lack of social grace and his bluntness, giving back as good as he got from Rodney in turn.

But the comparison ended there.

Where Yuri was all about the sex, with both of them using each other as a means of easing the boredom during the long, cold Siberian evenings and nights, he felt something far different with John. They shared so much more than just their bodies, spending time together watching movies and playing games, or even just talking, discovering shared interests in comic book heroes and terrible, old science fiction TV shows and movies.

After the accident in Siberia he had missed Yuri at first, but he had moved on - not forgetting Yuri but immersing himself deep into his work. Memories of John would not be compartmentalized so easily. He hadn't even left his bed yet, and he was already missing him, already wondering how he was going to go back to the lonely nights on Earth.

Atlantis had truly become a city of dreams for him, giving him almost everything he wanted from life - his work and someone to share it all with.

Deep in thought, he didn't notice John waking until fingers stroked against his skin.

"Hey," he murmured.

"Hey yourself." John pulled him down into a soft, closed-mouthed kiss. "You're thinking too hard." He kissed him again, breath a little stale but Rodney didn't care.

They fucked slowly, and Rodney kept his eyes fixed on John's face as John moved deep inside him, pushing him up the bed a little with every powerful thrust. He gasped as John caught the right angle, feeling sparks of pleasure shooting through him. Grabbing his own cock, he worked himself in time to John's thrusts, letting the pleasure build and build until he could barely breath, barely think, with all his focus caught and held in the intensity of John's eyes. One last thrust had him tightening his grip painfully on himself, his vision whiting out as he fell over the edge, feeling the heat of his own release coating his fingers and splattering over his belly and chest even as he felt John's hips stutter once, twice before John collapsed over him.

He gave him a small shove to persuade John to get off of him, feeling the mattress shift beneath them as John rolled onto his back.

"Fuck!"

Rodney almost sniggered at John's expletive because it was exactly how he felt - well and truly fucked, and not just by the physical act. The thought of giving up all of this and heading back to Earth was almost sickening to him but he knew he had little choice. The latest communication from Earth implied that Kavanagh was due to return imminently, and as much as he wanted to be here with John, he couldn't stomach the thought of working beneath that idiot. He had seen how hard it had been for Radek to work for Kavanagh so Rodney knew he would not last a week before he wanted to kill or maim the guy.

The problem with Kavanagh was his belief that just because he was highly skilled at one thing, that meant he was brilliant at everything. Even Rodney admitted to his own limitations, albeit reluctantly. He hadn't noticed John leaning up onto one elbow until John tapped him on the forehead.

"Thought I'd stopped you from thinking so hard."

Rodney snorted. "You did."

John settled back down and Rodney was surprised when he felt a hand capture his own, fingers threading. He squeezed John's hand, closing suddenly heavy eyes - and slept some more.

Three hours later, the chevrons lit up and as the wormhole settled, Chuck received a transmission from the SGC. On Woolsey's order he lowered the shield, and a few minutes later, dozens of people filed through the gate from Earth. Most wore the uniform of the various science disciplines and Rodney knew the others were soldiers simply by the way they held themselves. After the people came wheeled pallets piled high with equipment and supplies, occasionally being guided by more marines.

Rodney thought of all the requisition orders he had placed in the past two weeks, hoping that some of his requests for various departments were among those pallets. Within moments he was down on the gate room floor, ordering people in one direction and supplies in another to clear the area in front of the Stargate.

"I think I can take it from here, McKay."

Rodney turned, intending to remonstrate, when he caught sight of the speaker.

Kavanagh was back.

****

**One Month Later**

John loved Atlantis. He loved the beauty of the city with her graceful towers, and the steady hum at the back of his mind that told him he was home. He loved the Ancient technology that bent to his will by opening and closing doors on his mental command, and the gateships that obeyed his every thought. And yet the city seemed strangely cold and empty without Rodney's larger-than-life presence - or maybe it was just his life that seemed cold and empty without Rodney.

Sumner had not returned and General O'Neill had yet to assign his replacement so John still held command of the military. Surprisingly, Doctor Weir had not returned either, though John knew that was most likely a political move with the I.O.A. wanting to keep one of their own representatives in control of both the expedition and the city. John liked Woolsey though, sometimes sharing a whiskey and a cigar with him on the balcony just behind the control room that overlooked the city.

Kavanagh had walked back in and immediately taken credit for all of the work achieved in the city during his absence, despite Zelenka's contrary remarks to all within earshot. At first, most of the expedition had seemed pleased to see Rodney head out on the _Daedalus_ , almost welcoming Kavanagh back with open arms, and only gradually coming to realize what - or rather whom they had lost. Refusing to accept any of Rodney's ideas or plans, Kavanagh had changed most things back to the way they were before the _Daedalus_ arrived, and slowly the tension had began to fill the city again, full of disgruntled scientists moaning about a lack of equipment, space, or manpower.

Radek had taken to keeping John informed of all the science department's gossip.

"Miko threatened to pour coffee over Halper's head after he said unpleasant words about Rodney." Radek smiled. "For tiny woman, she is a force to be reckoned with."

John smiled crookedly at the thought of the tiny Japanese scientist with the big black-rimmed glasses cowering Doctor Halper.

"Do you miss him?" Radek asked.

John didn't bother to ask whom, as he knew Radek was referring to Rodney.

Radek continued on. "I miss my friend, and I miss his genius. I think you miss him too."

The words - _every day_ \- stuck in John's throat, strangely too raw and revealing to be spoken aloud, so he gave a half shrug. With the ZPCs powering the Stargates, communication with Earth took place daily and he received a dozen emails almost daily from Rodney - but it was not the same as having Rodney here with him. He could not reach out and touch him or feel that little extra hum in the back of his head from Atlantis whenever they were lying happy and sated in bed, with arms wrapped around each other. He sent small, pithy email messages back in turn but couldn't say all the things he would have whispered through a caress or kiss.

He and Radek talked a while longer but eventually John headed back towards the gate room, wanting to check in with Woolsey before going off duty as it was already quite late. As he approached, he heard the first of the chevrons encoding and he moved to the edge of the balcony over looking the gate room. He was pleased to see the guards had taken position even though the shield would remain up until they could confirm who was dialing in.

"Stargate Command," Chuck stated, and he lowered the shield on Woolsey's command. John was tempted to join Woolsey beside the gate technician's console until he saw a ripple in the wormhole. Moments later a figure appeared, and John's heart skipped a beat before leaping up into his throat. He moved to the staircase, taking the steps two or three at a time until he was standing on the gate room floor only ten feet from the new arrival.

"Rodney?"

Rodney dropped his heavy bags at his feet as John approached him.

"John."

It took everything John had to resist the almost overwhelming urge to grab hold of Rodney and hug him. He could feel Atlantis flaring up in the back of his mind and could swear the lights were shining just a little brighter. Rodney looked good, though a little uneasy, looking around the gate room nervously.

"You're here."

"Well, yes. Obviously."

"No. I mean... I thought you didn't want to work for Kavanagh."

"I don't. I won't," he added. He looked past John and John knew it was Woolsey coming up behind him.

"Doctor McKay. Welcome back to Atlantis. It's good to see you again."

"Yes. Well, it's good to be here."

"I've already prepared quarters for you next door to Major Sheppard's. Perhaps the Major could escort you to them."

John had not taken his eyes off Rodney the whole time, and he nodded absently, waiting until he could hear Woolsey moving away before he reached down and grabbed one of Rodney's packs. They walked towards the closest transporter in silence, with John grabbing quick glances at Rodney often, When he reached the quarters assigned to Rodney, he raised an eyebrow, realizing these were the ones with a sealed door that led into his own quarters.

The door opened immediately though John was unsure whether he or Rodney gave the mental command. John hesitated on the threshold for a moment before taking a step in so he could drop the pack just inside the door. He jumped a little as the door closed behind him and watched as Rodney stalked forward, recalling the first time they'd had sex. Rodney was the one who had bridged the space between them that time too, but this time John reached for him as soon as he drew close enough. This time John pulled Rodney against him as his mouth hungrily sought the taste and feel of Rodney that he had missed this past month. The pleasure of Rodney's strong body against his own was intoxicating, and when he next came back to his senses, both of them were half naked and sprawled across the bed in John's quarters, the door between their quarters wide open, and with them still kissing hard while their hands tightly held onto the other.

Almost giddy with growing pleasure, John stripped them both of their remaining clothing, enjoying the feel of Rodney's hot, flushed skin against his own after feeling so cold for so long. He leaned over Rodney, wanting to touch and taste every inch of skin within reach, until his own need drove him further. 

"I want you," he whispered harshly, and Rodney's only answer was a crooked smile and the press of bottle of lube into his hand, cap already thumbed open.

So desperate in his need to possess the man lying beneath him, John could barely remember slicking himself or preparing Rodney and yet when he pushed inside Rodney, he glided in easily, sinking deep into Rodney's body. He could feel Rodney's heels digging into his back, could feel the tight contraction of ass muscles as Rodney clenched against him, trying to draw him in even further.

"I missed this," he stated softly before leaning over to kiss Rodney. "Missed this so much." He kissed him again. "Missed you."

He thought he heard Rodney repeat his words back at him but as he withdrew an inch or two then thrust forward into the tight sheath of flesh, all he heard was a soft gasp and a whine of pleasure as Rodney urged him to go deeper and faster by digging his heels in harder and arching his back. It was all John needed and he found himself thrusting into the willing body, desperate to find release inside of Rodney after a month apart.

He felt Rodney buck against him, a familiar whine coming from the back of his throat as he came hard against John's stomach, adding to the slickness of the sweat trickling down both of them. Every muscle in Rodney's body seemed to contract hard with his orgasm, and it was all John needed to tip him over the edge too, hips snapping forward as he emptied himself deep inside Rodney in the most intense climax of his life.

Exhausted, he collapsed across Rodney, head buried against Rodney's sweaty neck, inhaling the clean scent that mingled with pungency of male sex. His heartbeat was hard and erratic, matching Rodney's, and he groaned when Rodney eventually shoved at him, aware that he was heavier than he looked. Reaching down ready to pull out, he was a little shocked to realize he'd not used a condom.

He glanced down to see Rodney smiling crookedly before holding up his hand to reveal a still packaged condom gripped loosely between his thumb and finger. He waggled the small package at John.

"Forget something?" Rodney asked.

"Sorry," he murmured, feeling uncomfortable even though he knew both of them were clean of any STDs.

"I'm not." Rodney's smile grew wider and softer, his eyes glowing with pleasure, only to ruin the effect by yawning widely.

"Sorry, sorry. It's been an incredibly long day. You wouldn't believe the idiots at the SGC," he started but another yawn overtook him before he could continue with whatever rant was building.

"Let's get you cleaned up and then you can tell me all about it."

"Sounds like a plan."

By the time John returned with a washcloth, Rodney was already half asleep so he cleaned him quickly before sliding back onto the bed and pulling the cover up over both of them. Despite feeling just as tired, John found it hard to take his eyes off Rodney, almost afraid that if he did then Rodney would disappear. Eventually he must have slept, and when he awoke the next morning, he grinned when he found Rodney snoring softly beside him.

****

The conference room was full when John and Rodney entered even though they were a few minutes early. John saw that Lorne had kept one seat open for him while Woolsey offered Rodney a second empty seat between him and an extremely happy Radek. Woolsey waited patiently until both of them had taken their seats before standing up to address the group.

"Gentlemen. Ladies. Before we start the meeting I'd like to welcome back Doctor McKay, who will be rejoining us as Chief of Science as of today. Doctor Kavanagh will be returning to Earth within the next few hours, and I'd like to thank him for his work on Atlantis."

John had noticed the murmur starting the moment he and Rodney had entered the room but now it rose higher. He caught Rodney's eye and saw Rodney's cheeks flush pink with embarrassment, probably because he had not said a word about it to John even though John's dick had been up his ass only hours earlier. Under the circumstances, though, John was happy to forgive him because it meant this was not some flying visit that would be over far too soon.

He barely heard the rest of Woolsey's agenda, hoping Lorne had been paying attention. Instead his focus was on Rodney, and on how quickly Rodney picked up the threads of the science department. The meeting ended quickly and John realized that his plan to wait for most of the department heads to file out was not going to work. Woolsey and a few others had managed to escape but most of the others seemed eager to speak with Rodney, no doubt recalling how he had got their departments motivated before.

Rodney stood up and yelled over the top of them.

"Listen up as I'm only going to say this once. I expect reports from each of you. Don't be pedantic, and don't be a smart ass. Don't leave anything important out as I will be grilling each of you over those reports. List priority requests and I will see what I can do about them." he glanced around. "Well? What are you waiting for? Those reports won't write themselves."

Everyone headed out until it was just Radek, Rodney and John left. John waited as Radek clasped Rodney's hand and welcomed him back.

"It is good to see you again, my friend." Radek looked across at John and smiled. "I will wait for you outside." He nodded at John and left quickly, closing the last of the panel doors behind him.

John walked slowly round the table. "Why didn't you tell me?"

"Because I gave my word that I would wait until Woolsey made the announcement... and also because I was rather busy at the time."

John smiled in remembrance.

"Chief of Science?"

"Oh, you haven't heard the best yet. Unfortunately, I'm sworn to secrecy on that too for another..." he glanced at his wristwatch, "...three hours."

That was the time of the next scheduled check-in with the SGC.

Resisting the temptation to tease the secret out of Rodney, John nodded. "Three hours."

Rodney hummed and rocked back on his heels, obviously pleased with whatever would be revealed in three hours.

"Okay. I can wait," John stated, hoping that was true. He resisted the temptation to reach for Rodney, knowing they had to keep their private relationship outside of their working relationship for the sake of the expedition, even if it wasn't a secret to anyone. With a nod, he left the briefing room and smiled at Radek in passing.

Three hours later, John tried to appear nonchalant as Chuck began the dialing sequence for Earth. He saw Kavanagh waiting in the gate room with his bags packed by his side and felt a twinge of guilt as he had never made that much of an effort to get to know the guy. Once Chuck had received confirmation that the iris was down on the SGC gate, Kavanagh moved swiftly forward and was quickly swallowed up in the blue of the wormhole.

Glancing behind him, he noticed a few more people had joined him beside Chuck, including Woolsey, Rodney and Lorne.

"Atlantis, this is General O'Neill. Is Major Sheppard there?"

John spoke up quickly. "Sir. Major Sheppard, sir."

"Good. McKay? You know what to do. Don't mess it up."

Rodney stepped in front of John and pulled out a small package. As O'Neill continued in a more serious tone, Rodney opened the package. Inside were two silver oak leaf insignia. Confused, John straightened as Rodney reached forward and removed the golden oak leaf insignia from John's uniform, replacing each with a silver oak leaf. Rodney stepped back as O'Neill continued on as if he was the one standing right in front of John.

"McKay, hand Lieutenant Colonel John Sheppard his new orders."

There was a time when he had coveted a promotion, but he had believed it would never happen after he received that black mark placed on his permanent record. Now that it was happening, all he could feel was shock and anxiety... and this was the moment he was dreading most. He had only just got Rodney back and the thought of being the one who had to leave this time was almost more than he could stand. He accepted the envelope, forcing his hand not to shake, and opened it, prepared to sacrifice his new rank if necessary. John had to read it through twice.

"Commanding Officer... Atlantis."

O'Neill's disembodied voice came through. "You have Doctor Weir to thank, Colonel Sheppard. She made quite the compelling argument for you. Don't disappoint me."

"Yes, sir."

The connection to the SGC closed down and after accepting the handshakes and congratulations from the others, John grabbed Rodney by the arm and dragged him into the transport and back to his - or was it their - quarters. He rounded on Rodney the moment the door closed behind them.

"You knew about this?"

"Yes. And no. I knew about the promotion just hours before leaving Earth. I had no idea what was in the envelope."

"If I'd been sent back to Earth?"

"I came here for you, John. Not just for the city."

John reached out and cupped Rodney's face in his hands. Slowly he leaned in and kissed him gently.

"Welcome to Atlantis," he whispered before kissing Rodney again.

END

**Works inspired by this one:**

  * [The Perfect Choice](https://archiveofourown.org/works/533028) by [Valika](https://archiveofourown.org/users/Valika/pseuds/Valika)




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